Because that's what makes it... film. It's hard to explain. Well, I do have an explanation that fits with Star Wars. In my opinion, the CG in The Phantom Menace stands out much less than those of the other two prequels, and that's because it was shot on actual film instead of the pristine perfect world of digital recording. Everything was so clear on digital that all the CG stuff just stood out, but a little bit of blur or grain made it more believable. Just like with the original trilogy, I never saw the boxes around the ships in spaces before I got the DVDs. On my tapes, they were imperceptible.

EDIT: That said, I don't mind pictures being cleaned up to remove age distortion (even though it's kind of fun to watch sometimes), or even to make it look somewhat better than it did originally. But I agree with battlewars that it can go a bit too far.