I think this would be a very good idea. I've been dreaming of this for a long time, now, actually :3.
I know games like Colleseum and Pokemon Stadium failed, but it wasn't because they were 3D. It was because there was little to no freedom. In Colleseum, your starter Pokemon were chosen for you. And you had a mission you had to accomplish. The reason all the GB/GBA/DS games were so popular was because you could catch and train any Pokemon. It was a way to express yourself. The Pokemon you raised reflected on what type of trainer you were. And best of all, there was no point where the game ended. Sure, your main goal was to beat all the Gym Leaders and defeat the Elite Four, but unlike other games, it didn't end there. Infact, there was still more to do! You could go places you weren't previously able to go, obtain new Pokemon you weren't previously able to obtain. And once you'd done all those things, you could begin training every Pokemon to level 100. That kept ya busy for a long time. (In fact, I don't think anyone's ever done that).
So I think if Nintendo made a 3D style game based on a GBA/DS style game, it would do very well. Think of it; running through fields and fields with your trainer, in a behind view. xD I think it would be pretty nifty. Another thing Nintedo could add would be the option to custimize your trainer with different clothes, skin color, etc. Then, when you had a Wifi battle, you wouldn't show up as some random Bug Trainer or Ace Trainer on your opponents screen.