How is Sonic CD different compared to the other Sonics? Every time I try to play it I am reminded of how bad it is and give up, so I don't know what you're referring to specifically.
But I have a good gamepad for my PC, so it's not usually a problem, although like every other gamepad in the world mine has the 4 button diamond layout like the emulated console versions would, not the 6 of the Mega Drive.
Its the choppy-ness that makes it annoying, on an actual console the game runs slightly smoother but the game engine is still crappy, Sonic tends to never go where you want him to, its very frustrating.
Sonic 1, 2 and 3K run much better on consoles, even the DS collection version is nice and smooth.