The Mega Drive is optimized for games only. It may be easier to code games for the system, but that's because the Mega Drive has a less complex GPU to work with than the Amiga OCS. However, it also means that the Mega Drive is much more limited with what effects you can pull off on that system.
Mega Drive uses a tiling-based method to render the graphics on screen, which is something the Amiga doesn't have. However, the Mega Drive's bit-mapping capabilities are very limited compared to the Amiga, and as a result, stuff like copper effects and onscreen colors, are sorely lacking in the MD. The Amiga has the ability to try and display more than 32 colors with clever coding of Denise. The MD doesn't have that capability. Don't forget the MD's limited memory and its' garbly sound.
Yes, the MD obviously had a lot of support throughout its' entire life, but so did the Amiga. Needless to say, Sega did throw a crap-ton of support for it's system with the Sonic games, their advertisements against Nintendo, and the fact that they didn't have censorship problems unlike Nintendo had at the time. Compare Mortal Kombat I on both MD and SNES, you will see the difference.