I am not a fan of 3D, and I did feel that much of the film was needlessly muddy with the glasses on, and that for the most part 3D did not add much past the title sequence. However I have not seen it in 2D to make a comparison.
The visual effects are truly astounding. For much of the film I thought the animals were real until it became clear that there was no possible way that these animals could have been trained to do much of what was in the film. There are only few brief shots in the film where the animals do not appear real. To warn animal lovers, there are scenes of animals in distress, but they are inherently tied to the nature of the story, and the animals are digital, not real.
It is also very rare to see a film which discusses theology and uses multinational and multicultural references in such a straightforward manner. This film is so much smarter than everything else in cinemas right now, it's a shame it is not being seen by more people. I was the only one on the theater at my screening. In many ways, this film is what CLOUD ATLAS (review here) aspired to be, but failed to bring to the screen.
Although to be fair, PI does not live up to one element of the hype: the movie does not prove or explain the existence of god. Of course, no movie (or book) could do that, unless you believe that god consists of the creative spirit of man. In that case, I have seen god this evening. And he is in fine form.