Hmm... what a pointless argument. Two systems based around the same CPU, but with the rest of their hardware design developed with completely different intentions.
The MD was purely developed as a gaming platform. And with Sega building arcade machines they put that knowledge into their 16-bit system, creating something that was good as 2D sprite manipulation and multiple field generation, along with 6 channel synthesized audio. Whereas the Amiga was a completely different beast with multitasking, one of the first systems capable of sampled audio playback (why would the Amiga need to generate sounds from a chip when it could just play back real sampled ones?) etc...
If you really wanted to compare the MD to something, the SNES would be a better choice. Then the MD would lose hands down. Try comparing some of the games that were released on both the MD and SNES for proof of that.
It always used to annoy me when people would directly compare the ST and Amiga to the consoles of the day. Each was designed with a different aim in mind, so the consoles would always have a slight edge in certain game specific areas, whereas full home computers still offered so much more.
And in general, most games were always the best versions on the system they were developed on. In this regard many of the games listed in this thread were initially Amiga games, such as Gods, and remain the best on the Amiga. Likewise all other systems have their exclusive titles that are worth playing just as much as any other. It doesn't matter what system you are playing a game on, as long as the game is good.