A lot of it comes down to developer support. A lot of segas games where made by sega themselves, ergo they had access to sources and sound and gfx, etc. Amiga versions of games were often done with no such help. Not just sega games either. Sega obviously had a lot of pull with other asian companies so would get more assistance than most.
The Megadrive is also easier to get the hang of coding wise. The amiga generally wasnt quite as easy to get the most from, but had a lot more scope for improvement.
There's lots of things an amiga can do better than a megadrive. Stardust 3d type sequences would be pretty much impossible on a megadrive (not enough gfx memory and poor bitmap handling). Amiga can display many more colors onscreen (not just copper gradients either, but real colors). Amiga deals with bitmapped graphics much better than the megadrive. Better sound on the amiga. A well done amiga game is much more fluid in movement.
Megadrive was a decent machine for the time (I actually have one of the fgpa ones and quite enjoy it), but in the right hands the amiga is more capable more often, which is pretty impressive considering the age difference between the two.
People keep saying that the megadrive was better for games, but it all depends on the games. Yes a lot of games that were on the megadrive where better than thier amiga counterparts, but the same is true of the reverse.