I just got mine today, and a word of warning to those who have both systems and are still undecided- the Gamecube version may have cooler extras, but the controls are totally counterintuitive.
For some ungodly reason, they decided to buck the tradition that's been in place since the NES days, and made B=Jump, A=Shoot. There's no option to remap them, either, and I'm having a hard time conquering 19 years of learned behavior. I was afraid of something like this... hopefully, I can still swap it out for the other version. I love you anyway, Mega Man.