I say it depends. For a new IP, they should go with the obvious choice when developing for a certain console. Example: I don't want to say that the Wii is a 2D machine, but 2D games on Wii work better than on 360 and PS3, right? Otherwise, we'd see those kind of games on XBLA or PSN. Muramasa would only be successful that way, you see.
If it's an old IP in need of evolution, and that the idea they have is to not "really" change the concept that made the old games successful, then I say going to 3D should be primordial. Just look at this example:
Gradius III
Gradius V
Obviously, Gradius V looks "awesomer." =P
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...
