Nobody in this thread would say that the cinematography was bad. The problem was that Kubrick sacrificed pacing and a coherent plot on the altar of creating meaningful, awesome-looking shots. The latter is partly Clarke's fault - the man was always much better at creating the feel of a science fiction novel than at writing an actual story arc - but it's hardly as though Kubrick made things any better.
I think many people are looking at this movie from the wrong perspective. They don't see a plot because they're paying attention to the story from the human point of view. But when I saw it (I've only seen it once, about a year ago, and I STILL can't get it out of my head!) I thought the 'plot' revolved around the Obelisks. Seen in that light, there is a very clear arc through time and space.
I also don't think that the earth obelisk caused the apes to evolve. Kubrick and Clarke are too smart to have such a simple idea of evolution. Rather, the obelisk is part of an early warning system to alert whoever put it there that some of the life on earth has started to invent technologies. And then the obelisk on the moon (chapter 2) alerts them that the earthlings have discovered space flight. And then the obelisk orbiting Jupiter alerts them that the earthlings have achieved the required stasis technologies for long-distance space-faring. The last scene shows that humans aren't prepared - biologically and psychologically - for some of the necessities of inter-stellar travel... i think

As for the pacing, I can't imagine the movie would have been better with shorter scenes (and camera shots that didn't last minutes on end! The whole idea of space travel is that space is, well, very big. Very very big, and it takes a long time to get anywhere. And the tension that the pace induced was criminal. Really freaky, for me at least.
The arbitrary camera angles reinforced the idea that there is no 'up' in space. There is no down. There is no perceived motion, so time seems to stand still. It was amazing.
I saw the movie on my 27" imac with decent headphones on. No distractions, and I was completely entranced. As i mentioned above, I think about the movie several times a week.
And to me, that's how I measure how 'good' a movie is. How often do I think about it after watching it? Are there still scenes in my head a month later? A year? Many years? And is it just a line or a scene, or are there whole emotional cascades of the feelings I had while watching it? By this measure it's one of the best movies I've ever seen - sequences are stuck in my head and won't leave.
just my two cents.
And in case anyone missed it, here's a link to a wonderful youtube of Pink Floyd's Echoes scored to Jupiter And Beyond The Infinite*. For anyone who likes this movie I can't recommend this enough:
http://www.youtube.com/watch?v=xQZAf97990w
*Pink Floyd were hoping to be asked to score the movie, but Kubrick had the final score done up along the lines of the music they listened to during editing as an audio placeholder, or so I heard