Well, I loved Finding Nemo and almost fell asleep during Shark Tale. In terms of visuals, I felt Finding Nemo had better and "cleaner" colors. Same happened with A Bug's Life and Antz. In terms of story, I think Finding Nemo's father-son relationship was more effective than Shark Tale's fish romance. In Shark Tale, I sometimes wonder why they bothered making it a fish story, since they basically mimic NYC and give the fish human characteristics (like how the fish stand on two "feet").
IMO, Pixar's movies (Toy Story, Monster's Inc., Finding Nemo, Incredibles) are generally better than Dreamworks and Fox's work (Antz, Shark Tale, Dinosaurs, Ice Age), with the exception of Dreamworks' Shrek.