Yoshi was seen testing with a Windows/xbox controller, including colored button indicators for it on screen. The special edition one uses the Windows controller layout. (if you are referign to the Japanese showing of the GameS one).

I imagine it will change the UI to fit various controllers, but some may have a default layout since not all follow the X B A Y RB RT LB LT format. (PC Side). Many Third Party ones do now.

THe PS3 version will of course be specialized to it's buttons.