I've always thought 2D was more stylish and fitting for the adventure game genre. But 3D is finally at a point where full-resolution 2D "textures" can be overlaid on the wireframes without compromise in quality, creating some very unique looking games.
In my opinion, "The Curse of Monkey Island" was the crowning achievement of 2d hand-drawn animated games. It was just so... perfect.
I have faith that LucasArts will surprise us one day with a new original game featuring hand-drawn 2d artwork. You'll see!