Tough choice, both were low points for me.
I'll say GameCube is better though, because even though Nintendo blew it with all these, Wind Waker, Mario Sunshine and Double Dash still easily beat Minish Cap and Super Circuit on top of the Lack of a new Mario game. GBA had Yoshi's Island though, which is better than all aforementioned games combined, along with an excellent A Link to the Past, but I can't really justify prefering a system of ports over one that actually had enjoyable newcomers like Luigi's Mansion.
Granted, the GBA has gotten a little more credit in my book because back when it was relevant, I missed Metroid Fusion and Fire Emblem. After having played them on 3DS I realize they are amazing games and I missed out on a lot. Maybe it wasn't all bad, and I just didn't want to see it.
As it stands though, GameCube over these two.







