As silly is it seems, i'd go with 2D, because 2D games were so amazing. You look at early FF games, and early Zelda games and everything that was packed in their so tightly (imagine what fun stuff could be done with a 2d game today now that the world is so much more dynamic).
3d is great and wonderful, and I do love it just as much, but I want to see someone do something amazing dynamic and awesome with the DS.
On a side note, LTTP in some sort of 3d remake would be sexy (FF3 on the DS?)