As with a similar topic, I don't pretend to know which is 'better', only which I prefer, and I've got to say it's the Megadrive. A massive amount of the SNES' landmark titles never made it over here to Europe, hell we didn't even get SMRPG, let alone FF IV/VI, Chrono Trigger or Earthbound. We got Lagoon though..
Streets of Rage 2, to me, runs rings around any beat 'em ups on the Megadrive, SNES or anything comparable, it's something I play regularly to this day. Soleil (Crusader of Centy) and Wonderboy in Monster World are both easy to beat and short, but offer some of the slickest, most genuinely fun gaming I've experienced.
That's not to say the SNES doesn't have a place in my heart or is in any way something I don't care about, Zelda III and SMW are two of my favourite games, but the MD's catalogue had a lot more interest for me. The graphics and sound of the MD wasn't a negative thing in my opinion, like a lot of its catalogue it reminds me a lot of slightly earlier games, which is no bad thing.