You can't really compare the two movies, I feel. It's two very different styles. The thing with final fantasy, in my opinion, is that they've put all their energy in the stunning CG-graphics, causing them to neglect the story a bit.I love monsters inc. for me it is even a lot better than final fantasy. ff was supposed to be for adults - but i still cant find the story behind the massive use of computer effects.
My personal favourite is also shrek, because it has great CG, great humor, and above all a super cool story. I'll spare you my comments, because they've all been mentioned above ...
Another movie which I really like a lot is Ice Age. I think it has quite a nice and funny story, and the characters are absolutely superb. If you look at Scratt for example, a prehistoric sabre toothed squirrel, think about it, who comes up with an idea like that? Just the idea of the sabre toothed squirrel is hillarious. The contrast between Sid and Manfred is just great. And the way they get the emotions out of Manny's eyes.
Well, that's all I wanted to say ...