I have no doubt that there were some things the GameCube could do better by sheer virtue of being a console (and thus needing to output higher resolution than a handheld), but the 3DS' more modern GPU is capable of achieving better effects in some areas than the Wii.
For all that Pokemon X and Y have done, they are an outlier in the weaker direction. Compare Mario 3D Land to Sunshine, or RE Revelations to REmake
Monster Hunter: pissing me off since 2010.