I'm not sure why people even mentioned SotB - worst game on any format IMHO.
Mr. Nutz is better on Amiga, as MD/Gen is completely different and less attractive game.
Even some MD/Gen games had worst sound, I like them more on console because of loading time and no floppy swapping.
SF II is better on SNES then on Amiga or MD/Gen.
R-Type (1 or 2) works much better on PC Engine then any other format.
Flashback is better on Sega CD, as intro and video seq are prerendered.
(same as 3DO, Jaguar and PC-CD Rom version of the game IIRC) Same thing with original Dune.
Mega Turrican (Turrican 3 on Amiga) plays better on Genesis. (because of controller)