2D........
Sonic 1, 2, 3 & Knuckles (Megadrive)
Sonic 1, 2 & Triple Trouble (Game Gear)
Sonic Advance 1, 2 & 3 (GBA)
vs
3D
Sonic Adventure 1 & 2 (Dreamcast)
Sonic 2006 & Unleashed (360/ps3)
Sonic Colours (Wii)
Sonic Lost World (WiiU)
No contest,...... apart from Sonic Adventure 2 & Unleashed, the 3D games have not been all that good, however, with 2D games like Sonic 1, 2 3 & Knuckles, Sonic 1, 2 & Triple Trouble, and all 3 advance games, its a comfortable victory for 2D Sonics IMO.
And i liked the 2D levels in Generations more than the 3D levels.