Ooh, now this is a tough choice, but I'm going to have to go with Banjo-Tooie. I know Golden Sun is amazing, but I'm picking Banjo-Tooie for a simple reason:
Banjo-Kazooie is in the tournament, and Banjo-Tooie is better than Banjo-Kazooie in every conceivable way.
Seriously! Gameplay modes, levels, dialogue, transformation, features, story, challenges, everything that Banjo-Kazooie did, Banjo-Tooie made a hundred times better. It became more than just a really good 3D platformer, but something of its own with gameplay changes, excellently designed levels, and overall more polish than the original Banjo-Kazooie.
Vote for it!