|capture from the "uplift" sequence at the beginning of Kubrick's 2001|
Jeffro's objection hinges on the question of whether it makes any sense for these ape-like human ancestors to "suddenly" be imbued with an understanding of tools by "divine fiat" via the alien artifact.
To be honest, this is a story element that rubs me the wrong way as well, but given the film's success and reputation in the genre I had to ask myself why.
On the face of it, it seems a not unreasonable premise for a science fiction story - and in its favour it resonates with the questions that were surrounding human evolution at the time both the book and the movie came out.
The core of 2001 is of course Arthur C. Clarke's short story The Sentinel which he apparently wrote in 1948 as his entry in a BBC competition.  But this story only contains the seed of the idea, and forms the basis for the scenes on the surface of the Moon where the first Monolith is discovered in the film. The rest of the film, and the book that was developed along with it  were grown from this seed, and are very much a product of the late 60s in many respects.
At the time the film was made, we knew much less about human evolution than we do now.  The evidence we had at the time showed what appeared to be a sharp division between clear human ancestors (Homo lineage) who were using tools and fire and clear extinct great ape lineages who we thought were not  - ideas proposed to fill this gap ranged from special creation by supernatural agency through to a chance mutation that just happened to have "the right stuff." In between, some exotic evolutionary histories were "floated"  including Zecharia Sitchin's ideas on alien intervention.
On top of this, the late 60s saw deep interest in altered consciousness  and a growth in interest in alternative ideas. In this context, it's hardly surprising to find that evolutionary gap being plugged by what we now see as a rather silly idea  and accompanied by what amounts to a glorious on-screen religious experience.
Given this context and the fact that we accept even sillier ideas without blinking in other SF works, why should this seemingly innocent conceit be troubling, especially in a film that was received very well and raved about ever since? 
I think the issue is that "science fiction" is a rather large tent and although 2001, Star Wars, ERB's Mars stories and War of the Worlds are all stamped SF they actually operate under different rules.
The Force is acceptable in Star Wars because, despite being dressed up in space ships, blasters and robots, it's actually a fantasy so it operates under rules that demand resonance with mythic archetypes. So long as it's internally consistent, a lot of the tech etc can be black-boxed without issue. (contradicting Ben Kenobi is an example of a failure to be consistent and as you point out it causes problems)
ERB's Mars stories are similar in that the world John Carter travels to doesn't have to be Mars - it just happens to have that sign hung on it. Beginning to end, it operates on mythic levels so much can be accepted so long as it's internally consistent.
War of the Worlds again doesn't need Mars - that's just a convenient label that forestalls questions as to the origin of the aliens. The point is the vastly superior tech of the alien invaders, the bumbling, over-confident early response of authorities, and the irony that the aliens are defeated by the fact we're too backward to have conquered microbes. The tech presented is a reasonable extrapolation from things in use or being discussed at the time, in most cases, and the main thrust is the social reaction anyway so we can call this sciencey science fiction.
Here's where the problem lies:
Most of 2001 appears to be presented as a science/engineering hard SF story. There's solid extrapolation, the tech itself and scientific advances are integral, and it appears to be a science mystery. The scene with the "space flight attendant" delivering a meal, the meeting on the space station, the Moon excavation site with the Lunar Monolith, the suspended animation and other tech of the Discovery One en route to Jupiter/Saturn 
With the "discovery" of the orbital monolith it becomes a first contact story, and to be honest the presentation of the aliens being so far advanced that we can't even grok them outside a psychedelic experience works, especially in historical context.
However, the premise of "uplift" as the moment of transition from ape to human is jarring in the context of the majority of the film. It's not an entirely unreasonable riff on the more out-there ideas of the day, but it's out of step with the majority in the middle - because it breaks the rules:
It invokes mythic themes and deus ex machina in the context of what's written as a solid engineering SF story. To my mind, this essentially puts the film (and the co-developed book) in the position of being two quite different stories which have been stitched together, which I think is what causes the slight sense of "wrongness" that rubs me the wrong way in the early ape scene and the transition to psychedelia at the end. 
Were I to be tasked with "fixing" the problem  there seem to be only two ways to go:
1. Cut the initial uplift scene, present contact with the aliens at the end as written but make the "descent into madness" less abrupt.
This makes the story a "hard SF" story about the implications of first contact and the smallness of humanity in the context of the universe. This is a well-tried theme, yes, but to be honest I think that a version of 2001 that had taken this route would have rendered Sagan's Contact unnecessary - in fact, it would appear a rather wishy-washy effort in comparison, I think.
Consider: we are treated at the beginning to a paean to humanity's technical achievements:
- Travel to LEO and the LaGrange space station is so casual that Floyd is dozing in front of the picture window and an in-flight meal is served in exactly the same way it would be on a long-haul business flight.
- The space station itself is so basic and obvious a thing that it has lounges in the corridor. There are hints that there are bars and cafes just off screen. Certainly, they seem to have nearly unlimited access to Retro Modern style furniture catalogs!
- While it does seem as though everyone we meet has at least one PhD, this is also portrayed as fairly ordinary - what kind of future is this in which people have the luxury of nearly constant study?
- While the Moon excavation is clearly a grand thing, the implications of being able to bring such an industrial effort to the Lunar surface are stunning (or should be) - the infrastructure and comfort with working in space is amazing.
So here we have a society that has developed to the point where rather a lot of people have the luxury of pursuing intellectual interests to quite high levels, and technologies that in the 1960s were strictly speculation have become as casual as air travel and hanging out at Starbucks. Amazing, right? But there's more!
We learn that not only have we cracked cis-Lunar space and made it our own, but we are pushing to what seem to be the edges of what is possible to be known:
- The artificial intelligence HAL is displayed as not only a crown jewel of computer advancement, but so well developed that it's trusted as the caretaker for a human mission to the outer solar system.
- We've so mastered biology that suspended animation is considered a viable option for the Jupiter mission.
Think about this - to make a truly human-like AI such as HAL is portrayed to be suggests a rather deep understanding of the human mind, which in turn suggests that we think we are getting close to understanding our own "inner space" very well indeed. On top of this, although the ability to suspend life via "deep freeze" is portrayed as being used for the first time on this mission, it's trusted enough to do this not with a "test pilot" crew but with the actual primary mission. Can suspended animation missions even further out, perhaps even to the nearest stars, be very far behind? Even the space ship Discovery One suggests this, being equipped with a new kind of thruster that has allowed the mission to reach Jupiter in an amazingly short period of time.
Clearly, humanity is being portrayed here as entering a glorious future of mastery over everything we could touch - and it's the shock of discovering just how backwards we still are that makes the story. Indeed, it's the whole point of the story that started it all in 1948.
So: take this scenario, wow the pants off the audience with this truly incredible - and completely plausible - high tech future, take advantage of Kubrick's mastery with the camera to impress us not only with the vastness of space but with how effortlessly we seem to be conquering it. We're set up to be the rulers of the universe, right?
But then we discover the artifacts. We're shocked by the discovery we're not first, but even so the artifacts appear to have been left long, long ago  by someone who is long gone. Aha! So we're the inheritors, and perhaps there's a message here for us?
We investigate, but the more we learn the stranger things get, until at last we're dragged kicking and screaming into the realization that we really are just "pathetic earthlings, hurling our bodies out into the void without the slightest inkling of who - or what! - is out there."  This is the point at which the transcendent experiences can be presented, showing how we're just not capable of comprehending what lies beyond the veil, we're just not ready to inherit.
In this way, the story falls firmly in the "engineering SF" category, with some "plausible speculation" at the end that permits some philosophical musings.
Now, this is obviously part of where Kubrick and Clarke were going with this film, so it's an easy hack. It's also clear that one purpose of the opening scenes is to serve as foreshadowing of modern humanity's stature in comparison to the Monolith Makers - like these apelike ancestors, we're reduced to hooting and shrieking our awe and incomprehension.
But the other purpose of those scenes is the problem - they're used to tell us that the very reason there are modern humans, the reason we have this talent with tools, is because the Monolith Makers gave it to us.
To me, this element of the message practically repudiates the whole "look how great we could be" engineering SF message of the rest of the movie and reduces the stunning SFX and implied setting to a footnote in service to the overarching "creation story" elements. This is where the story rubs me the wrong way, so to be honest I think that in rewriting the film to be a true "hard SF" story I would be forced to either rework these opening scenes significantly (eliminating the monolith for example) or cut it entirely.
2. Keep the uplift scene, but add more "fantastic" to the middle.
But let's say we like the whole uplift/special creation elements  - can we remake the film in that way instead? Absolutely!
We could keep much of the technical prowess demonstrated in the film, but it would have to recede into the background, be completely dominated by the human element. More importantly, if we're going to be playing with this mystical theme I suspect we need to inject more mysticism into the body of the film. This would lead us up to the transcendent experience effects at the end as well as underlining the "special creation" dimension.
The religious experiences at the end would need to be echoed in some way - we can retain "the transcendence of the apes" at the beginning in this case, but we can also touch on the theme again and again through the body of the film - perhaps by revealing clues that emerge from archaeology: this is veering into Sitchin's territory of course, but it's not unreasonable for this kind of mystical speculative fiction.
Moreover, I think there would have to be a stronger case for humanity as "special" all the way through - possibly by capitalizing on "religious experience" as a means of unraveling the mystery, portraying the ancestors who experimented with trances and drugs, who made such artifacts as the crystal skull, who built monuments like Stonehenge and Easter Island as being in touch with something deeper and more mysterious. We might also show humanity beginning to master "psychic" forces - and this could even be woven in as legitimate SF, capitalizing on the fact that the CIA and KGB were (apparently) seriously looking into things like remote viewing and telepathy. Presume that at some time in the future these experiments - and experiments with psychedelics - pan out, wrap it up as a new branch of human knowledge, and now we really have an argument for human specialness.
This sets the scene as the human mission makes its way into the outer solar system to investigate, and makes it possible for the closing transcendent experiences to be more comprehensible - in fact, it almost demands it.
Where the "engineering SF" version ends with humanity learning that we're just not ready to understand in the face of a new frontier we didn't even know existed, this version would logically end with humanity being invited across the threshold to join the true masters of the universe - it's in keeping with the almost alchemical tone of hidden secrets and special powers that "sublimating" to the next phase involves embracing the fact that in this new world we're just infants.
The message here could be given more explicitly, perhaps with a religious-experience-like exchange with our "elders" - in this version of the story we get a solid "fantastic SF" tale about mythic origins, hidden history, and humans as the chosen heirs of transcendent aliens.
You will notice, of course, that these are two very different stories. I think that many of the same "beats" could be used in each film, but there are layers of meaning different in each approach, and of course they each are working toward a very different conclusion.
The thing about the film as it is that rubs me in a funny way is that it appears as though Kubrick and Clarke were trying to have their cake and eat it too.
They wanted to make a grand, glorious hard SF masterpiece, a monument to what they saw as the ultimate conclusion of the enormous technical strides that were being made in the 60s. They wanted to paint a future beyond the nervewracking nuclear worries of the day, where a (more or less) united humanity stretched out its hand to touch the stars...and learns just how small we are. This is long before Sagan's famous "pale blue dot" commentary of course, and even before the comments of Armstrong and Aldrin and Collins after they first looked back at the Earth from the Moon, but we had already heard the wonder in the voices of astronauts who had been in orbit and we were starting to get a true sense of the enormity of it all. I think this is what they were trying to capture through most of the film.
But they also seem to have wanted to create a transcendent SF work, a "religious" experience embedded in the sterile human world of technology.
It's perhaps important to note here that Clarke's work frequently has religious themes, and in fact he had a long courtship with the paranormal that seems to have ended in the 80s or early 90s. Clarke described himself variously as a pantheist (what he insisted be printed on his dog tags when he was in the RAF), an atheist, and a crypto-Buddhist (though he always maintained that Buddhism is not a religion) but his work actually explores all sorts of religious ideas, and this in combination with his fascination with the paranormal I personally think reflects a deep interest in the nature of self and identity, and actually was probably born out of his rational, scientific outlook on life and an openness to exploring whether mystical or paranormal ideas might have some foundation in fact.
Likewise, Kubrick himself has said that he didn't intend the film to imply "God" but rather that it's an exploration of the possibility that there might be intelligences in the universe so far removed from us that for all intents and purposes they might appear to be gods. In fact, he has been quoted in an interview with American Cinematographer as going so far as to claim that the entire film is a refutation of the idea that there might be a god, saying:
"This film is a rejection of the notion that there is a god; isn't that obvious?"
Given this knowledge of the attitudes and ideas of the two creators of the film, it seems unlikely that when we say "religious experience" they would have made a version of this film that literally required the experience to be religious, so reinterpreting elements of religion as being echoes of some kind of species-level memory, or even deliberate messages from our "sponsors" would seem to fit with the sort of thing they might consider using to generate a mythic version of the story.
Honestly? This is a very complex film. It famously has far more non-dialogue scenes than dialogue scenes, and so is almost entirely a visual work - it's incredible how such complex ideas can be communicated via nothing but (admittedly incredible) screencraft.
I enjoy this firm very much every time I see it  but I'd be lying if I said I completely understood what Kubrick and Clarke were aiming for. This really is a great film in my opinion (though of course I am biased [see 8 again]), and I certainly wouldn't demand it be "remade" to "fix" the dissonance that bothers me. [see 12 again]
But the fact is that two very different stories are being attempted here, and to me they don't seem to go together - the "rules" for each clash, and realising this can, I think, help to improve our own efforts. The take-away, basically comes down to this:
1. SF stories (all stories, really) can be divided into clear types
2. These types have their own unique "rules of engagement" that follow from their foundations and the expected internal logic.
3. It might be possible to mix types (and therefore rules) but it will be a tricky process, and you will risk jarring the reader/viewer.
If we look back, I think we can see a number of films and (less often) books that famously suffer from criticism that can be traced to just this jarring effect - for just two very obvious examples:
Star Trek V: The Final Frontier - takes the "black box sciencey" core elements of the Star Trek universe and tries to graft on quasi religious themes, including a rather ridiculous interaction with "god". While Star Trek had explored the nature of gods and beings far beyond mere humans in the past, the way in which the matter was engaged in this film was more mythic than materialist, and it rubs many viewers the wrong way. (the film obviously has other flaws as well, as a wealth of critical reviews are quick to point out)
Star Wars prequels - I won't get into the weeds here, as there are many things to critique if the Internet is to be believed, but one element that gets routinely mocked is midi-chlorians. You might think that anyone who freely accepted the concept of the Force in the original trilogy shouldn't get so worked up about these microorganisms that apparently are the conduit between intelligent beings and the Force - but the issue here is again a mismatch between the sort of story Star Wars is (fantastic SF with strong mythic elements) and the nature of the midi-chlorian speculation - by trying to explain the Force "scientifically" in something approaching real-world terms, the films clash with the mythic elements and the result is an almost visceral reaction in some people.
As 2001 shows, even when blended by masters like Kubrick and Clarke, the combination of different story types can cause issues. 2001 works but the clash causes a roughness that wasn't necessary.
The type of story you're trying to tell is important - not because some types are superior to others, but because it takes a very, very careful hand to blend types successfully. You must be aware of what you're doing and think through the implications very carefully, or you will be courting disaster.
1. The story apparently failed to place in that competition, but was subsequently published in the magazine Ten Story Fantasy in 1951, and republished several times in the next 2 decades. The apparently out of copyright version of this story is available online here.
2. An early example of book-film marketing tie-in.
3. Remember, the book was written concurrently with the making of the film, and the release in 1968 is long before important discoveries in paleoanthropology that inform our thinking now: Australopithecus spp were only just being accepted as human ancestors, and Homo habilis had only recently been accepted as a separate species.
4. In the 60s Jane Goodall's research was only just beginning to challenge the perception of chimpanzees as purely vegetarian foragers, with evidence of tool use and complex social structures that could be compared to humans.
5. Gratuitous pun referring to the Aquatic Ape "Theory"
6. This was perhaps the peak of Timothy Leary's popular visibility.
7. New information on tool use among non-human primates and even other more distantly-related animals, as well as new information on the human lineage itself makes the shift from pre-human to human more obviously a gradual one, eliminating the need for a "missing link"
8. Full disclosure: I have a soft spot for the film myself, having seen it in the ship's cinema on an Atlantic crossing. I'd already been introduced to SF&F via Doctor Who and Star Trek reruns on the BBC, and having been
9. The destination changes between the books in the series, but was Jupiter from the first in the film.
10. Is this a spoiler? They knew there was an "anomaly" there when they sent the Discovery One in the first place.
11. Let me be clear: I actually really like the Thus Spake Zarathustra ape scene at the beginning, and could be persuaded to like the closing religious experiences (which are actually not a bad surrealist pastiche) but they clash with the bulk of the film.
12. Which I won't be. And to be honest, I would mock and revile any effort to remake the film anyway.
13. Yes, we can now get out to Jupiter in about a year - see the New Horizons mission, using a direct route (Galileo took 6 years using Hohmann transfers) - but at the time Apollo-type technology was the best available. Saturn thrusters accelerated Apollo mission vehicles up to 25,000 km/h at launch, but the crewed vehicle travelled at speeds of between 2,000 and 5,000 km/h for most of the journey to the Moon. At these speeds, it would have taken a crewed vehicle about 10 years to reach cis-Jovian space. Discovery One was truly travelling at amazing speeds, even for us now.
14. But not in a galaxy far, far away, thankfully.
15. cf The Imperial Vortex.
16. To be clear, I don't actually think there's anything wrong with it - I just don't like how it clashes with the rest of this particular film.
17. I tried to find the origin of this quote, but sadly the original publication seems not to be digitally extant, and the only source cited seems to be Warren Smith's 2010 book Celebrities in Hell
18. Despite the fact it underscores the promises that we'd be on Mars in the 80s and into the outer system by the early 2000s. Promises that were still being made when I started being seriously interested in SF, but which had died by the time I was old enough to really appreciate it. Killed by the Reagan era, really.