megadrive had the 2 scrollable layers plus the "window" overlayed and I don't know how many sprites on the megadrive, I'm sure wikipedia has the answer
the amiga had better sampled sound output, but the megadrive had more sound channels, and it's nice to be able to hear sound effects and game music at the same time
I couldn't really say which is "better" tho, I guess it just depends on what you doing.
I reckon a megadrive has the edge on the 500 at least for 2d games, but it's still down to the skillz of your programmers.
I would suggest comparing the typical games that came out on both systems year by year to see what was better.