Back when they were new, I was one of those "Adventure 1 is best" people.
After replaying both though... it's Adventure 2 for sure.
1 is better in a lot of ways, but 2 is just a tighter game. Tighter controls, 60fps, longer Sonic levels, better Chao garden (especially with Battle's improvements, though the gardens got a little smaller). The emerald stages were worse, but I liked the shooting stages better than SA1's.
Also SA1 had fishing... awful awful fishing stages.
Amy was unique but they barely used her at all.