Same here, Metroid Prime introduced me to the series. I prefer the second game and love fusion as a close second, followed by Prime 1 (that may as well be tied). I have far less of an affinity with Super Metroid, though I recognize just how good of a game it is outside of nostalgia goggles.

Weird, the wii controls were never an issue apart from the remote losing connection from time to time. Then play the gamecube version and forego prime 3.