I had both systems, and enjoyed both of them for differenr reasons., But genesis gets the edge for the following reasons:
Better controller (6 button)
Better software generated sprite scaling
Allowing for blood and violence (absent from nintendo until 1994)
Better sports games
Better line scrolling/parallax scrolling
The sega channel
Just watch the video where Nintendo was advertising how colorful their console was. Then one of the Sega representatives came and showed them Sonic the Hedgehog. The color difference was apparent, and Sega was the winner. Seriously there goes one of your only advantages. So that leaves what little else Nintendo had that was "better."
I can still remember the day in 1993 when I switched on my Mega Drive for the first time. I still do it once in a while for nostalgia (emulators work better than the actual hardware, but they don't give you the same feel). It's more a matter of heart, I prefer the Mega Drive and its first party games (3rd party Ghostbusters) over the Super Nintendo, the only exception is for Link's Awakening (and 3rd party Final Fantasies)... It's almost an even score, but now you know where my heart goes.
It all depends on your point of view on video games, and which system gives you more nostalgia. For me, that's the NES. For others, it's the Megadrive/Genesis. I love Nintendo, while others love Sega. It all depends on your style and which console you like better. Some people can't choose and love both.