Definitely 3D.
It's hard to see good facial expressions on little "things." RPGs are all about story, and even if you can portray how the characters feel by just reading tons of lines of text, you still need expressions on your characters.
Then again, games like Chrono Trigger and Star Ocean are a bit different. The developers put "expression bubbles" on top of characters to express how they feel about a certain situation going on. It's just attention to details like this that makes everything more memorable, especially in the character development part of the story. I guess some 2D RPGs are "special!" =P
Also, most 2D RPGs have turn-based battle systems, which I don't particularly favor. 3D can bring new ways to make battles a bit more intuitive.
Random game thought :
Why is Bionic Commando Rearmed 2 getting so much hate? We finally get a real game and they're not even satisfied... I'm starting to hate the gaming community so f****** much...
