I agree with what A-non-a-mus just said. The characters are just so much more alive and pleasing to the eye as well as background images and so forth. (Did anyone notice how how "flat" personality wise the characters in Finding Nemo were, no depth! They depending on there cutesy looks to get them through the movie, pathetic!)
Besides 3D is only what a computer can do, where as 2D includes many people working hard and really believing in the project, it's what the person can do therefore it's much more satifying to them when the project is completed, they can step back with a smile and say,
"I animated that!" and they really did animate it, they worked long and hard for about a week to get a 5 minute scene but look how much it means to them. Face it 2D is just better!