I don't know how someone can love this era and not be enthralled by both of these. They have different advantages, but that's part of the charm of the era and they complement each over nicely.
The SuperNes only barely edges it out since I prefer Nintendo as a developer over Sega (At home, at least... Sega is hard to beat in the arcade) and the SuperNes is what I had as a teen (Didn't buy a Genesis until the Genesis 3 appeared from Majesco). There are so many fine games here that I'd miss out on if I just stuck with my Super Nintendo, such as this top notch port of Roadblasters that has kept me occupied lately.
https://www.youtube.com/watch?v=3hFtt533unc
Minus a slightly different sounding engine note and the removal of the tiny bit of voice work in-between levels, it's virtually arcade perfect.
The 3D there is extremely basic and not at all a good example compared to stuff like this. I'm not even sure the space ships in there are actually composed of polygons, or just 2D sprites being scaled and rotated. And heck, look at that huge border and the tiny amount actually going on in the gameplay window, yet it still seems choppy.
It's especially impressive when you look at the game it was a conversion of on the Amiga.
https://www.youtube.com/watch?v=BVKDvLM8pKw
https://www.youtube.com/watch?v=RRnA-_UCxJU
They got remarkable close to it as shown in the former link, compared to the latter that was a dull, full 2D, sprite scaler on the SuperNes (Where as the more substantial trackside objects in the Sega version are obviously composed of polygons).
The Genesis was the place to go for 3D. I think the lineups kind of bear that out as well such as all the flight sims on the Genesis where as the Super Nintendo is devoid of any (Unless one counts something like Pilotwings or Wings 2 as flight sims... I'm thinking more along the lines of Mig-29 on the MegaDrive).