Sonic Adventure 2, as to this date, it still has the best portrayal of Shadow and the best grinding mechanic. It all really started to go downhill starting with Heroes. After a decent start in 3D, they just butchered everything. Which is funny, you'd think it would be the other way around, that they improve over time.
Heck, you can barely call the recent games 3D, as like 50% of the stages play in 2D.