as Paradox stated, there's really nothing wrong with Pokemon in 3D. Colloseum and XD are still simple, turn-based RPGs like the portable games, and the developers just wanted to experiment with something new. The gameplay's more or less the exact same thing. Sure, you don't go around collecting gym badges or finding wild Pokemon in the grass, but it's still an RPG with the same battle system. If anything's wrong with it, it's that they couldn't take more advantage of the game being on an immensely more powerful system, but since they didn't, there's really not much of a "transition" from 2D in the first place, is there? They very well could've just released these games, with the Dark Pokemon plotlines and being able to Snatch from trainers, on the GBA, and if they did that, you'd all probably still be demanding a 3D RPG, wouldn't you?
Anyway, I agree with Paradox, best transition is Zelda, worst is Sonic. Zelda's main concept has always been about having a world to explore, and now that the franchise is in 3D, you just got a more realistic environment, and a bigger world, with which to do so. And the battle system, with the targetting, was pulled off rather flawlessly, unlike Sonic, where the homing attack will often glitch and send you falling to your death. The 3D hasn't exactly done wonders for the high-speed gameplay, neither. Doesn't help matters that Tails and Knuckles are constantly getting the shaft, being shoved in some mech or doing tedious treasure-hunting. At least the Adventure Fields let me do some old-fashion exploring with Tails (something I loved in S3&K).
I'd also say Mario, but only because I miss the power-ups (which don't go away after a set amount of time, but rather when you get hit by an enemy, which wouldn't happen if you're careful) and being able to ride a Yoshi that won't die from touching water, of all things. Levels where I just go from point A to point B rather than doing some mission were nice, too. Otherwise, they seemed to have gotten the traditional gameplay of platform jumping and such down pat.
