Boy, oh boy.
Tough choice. Two of my favorite games, squaring off - Viewtiful Joe and Mega Man Legends 2.
For my money, MML2 was the perfect way to transition a traditionally 2D series into 3D and do it right, joining Mario, Zelda, and other franchises that made it work. The game was a blast, with a fun and dramatic story, the memorable characters, great gameplay, and the old school Mega Man feel fans loved from the original games. It was everything I could have asked for, and it sucked me right in. I played it again recently just to make sure it was as good as I remembered and it absolutely was.
On the other hand, Viewtiful Joe was a clever, intuitive 2D beat-em-up with a sense of style and flair unlike any other game I have ever played. The music, the art, the story, and especially the gameplay made it one of the freshest and most interesting things to happen to the Beat Em Up genre since Streets of Rage 2.
In the end I voted for Viewtiful Joe. MML2 is amazing, but Mega Man Battle Network 2 is better than it and it's already in the tournament. Viewtiful Joe gave us frantic action, slick graphics, and never-seen-before gameplay elements. In fact, the only thing it lacked was co-op play.
Henshin a-go-go, baby.