Both are great, but 1 is a better, more focused game. 2 had some awkward hubs and couldn't quite figure out what all it wanted to do with the characters, plus a few glitches and bad design choices they didn't have time to iron out. (3 is a much more polished version of 2's concepts, IMHO, but people seem to think of 2 as better for some reason, maybe the mini-game ADD puts them off.)
One of the things I liked about 1 was that, for a platformer, you could unlock features and abilities that were useful AS you progressed during the game, not after the fact. For example, the immunity to falling and water injuries made that croc sequence so much easier. Usually platformers only give you immunity to something once it doesn't matter anymore.
I never beat those Master Thief Time Trials, though, I remember they were brutal. I should probably go back and give them another shot sometime.