Overall I like the SNES version better of MK over Sega for these reasons:
-Better controller, I think this goes without saying vs the SG controller which only had 3 buttons and start to block was just not practical and then they realized this so they made the 6 button controller. But yeah SNES controller was perfect for MK and SF, but especially for MK with the block being in the perfect spot and HP, LP,HK, LK etc being much better than the SG controller.
-Graphics, the differences are pretty obvious when you have them side by side. MK looks better on the SNES than Sega, better graphics, colors etc easily.
-Sound, again something the SNES version does better than the SG easily. Sega sounded tinsey, higher pitched just sounded weird. The SNES version had much better sound, more accurate to the arcade. Neither were arcade exact port accurate but the SNES cleary does the better job.
-Gameplay, ok the gameplay is pretty smooth on both but I feel like the SG version is MK on speed(some people like that, I don't personally) the SNES version felt a lot more like the arcade to me than the SG version in terms of closeness to the arcade port gameplay wise.
I played both a lot, I have to say out of all of them for both consoles. Played MK 2 easily the most on SNES. At my house, my friend's place down the block we'd play for hours every day, looking for EGM and Nintendo Power for the secret finishers, fatalities, animalities, friendships etc(back before the days of the internet)
Comparing each game in terms of accuracy to the arcade port.
MK 1-Ok, the Sega version winded up selling more due to the infamous blood code which Sega hid in the game so the fatalities were like the arcade and this gave them an edge on the SNES version of MK since at the time, Nin was very anti blood, violence etc. However, gameplay wise the game felt better on SNES than the Sega G which again felt too fast.
MK 2-Nin pretty much learned from their mistake and said fuck it, let it rock all out and pretty much destroyed the SG version as a result, better gameplay, graphics, sound and 100% arcade accurate. It wasn't even close.
MK 3-This one played nearly identical from what I recall on both, though again the SG being slightly faster. I would still give the SNES the edge here due to the gameplay, graphics, sound and controller as the run being L helped bigtime while R remained block. I mean hell, even now consoles like PS and Xbox both took the SNES layout from the 90s what's that tell ya?
UMK3-Ok, while I enjoyed this game more on the SNES personally due to again the configuration, pad and graphics, sound. The gameplay I believe was actually more arcade accurate on the SG version believe it or not. The one game out of all of them that did the better job than Nintendo in terms of gameplay being better. I would still prefer the SNES controller however, but yeah in terms of gameplay I seem to recall it being better/more arcade accurate on the SG.
So overall, I'd say SNES takes it over SG MK games 4-1 overall. The MK series on both were fun, fluid in their own way but if you're a guy who cares about graphics, solid controller, dpad, sound and better gameplay. It's pretty obvious the SNES was the superior version overall. BTW, I had both, my SG broke though I still have my SNES just not hooked up. I modded my SNES classic mini with both versions of the game with UMK3. And the rest SNES versions.