I just think the homing attack has become part of Sonic's moveset. It makes sense in the 3D games since even in a game like Mario Galaxy, it is hard to exactly land on an enemy. It's in the 2D games because it was a big part of the 3D games. And again like Mario, NSMBWii had the spin move out of Galaxy, and the newer 2D Mario games have other moves from the 3D ones as well.
I do think it sucks for the 2D sonic games, though, but Colors (and Unleashed) would switch between the perspectives frequently, so they can't exactly have it work one second and not the other.