As a teen living in the 16-bit era, I was one of the rare few who owned both, a Super Nintendo, and a Sega Genesis. The SNES had a better processer than the Genesis, but the Genesis had it's share of superior ports, as well. Arcade ports have been made available on both machines, and I remember to this day which system had the best port.
Captain America And The Avengers: You'd think that this game would resurface with the release of The Avengers. The Sega Genesis was the first to have a port of this highly awesome arcade game, especially since the port was handled by the same company that gave us the arcade game, Data East. The SNES didn't get a port until the game was licensed to Mindscape. I was expecting the SNES game to blow the Genesis game out of the water. Sadly, it wasn't to be. The SNES game was highly unplayable. Best to stick with the Sega version on this one.
Mortal Kombat: I have played both versions of the original. The SNES game was closer to the arcade game in terms of graphics and sound, yet Nintendo decided to censor the game, taking out all the blood and gore. The Genesis game kept all the blood and gore intact, though you needed a code to get it (for those that need a reminder, it's ABACABB), but it's one step shy of playing on 8-bit. The only voice sample in the game was "GET OVER HERE!" So there is a lot of give and take in both versions. The Sega version outsold the Nintendo version due to the censorship, so Nintendo thought it over and allowed Mortal Kombat II to have the blood, making it the best port ever.
Revolution X: This game was ported to the SNES, Genesis, and Sony PlayStation. That being said, the PlayStation version was just shy of owning the arcade machine itself. The other two were made when the 16-bit era was coming to a close. Both versions were having a hard time keeping up with the arcade styled play. The Genesis and SNES had a hard time scaling in this game. It goes without saying that SNES version is the easiest to get through with a perfect ending. Having played both, I'll stick with the SNES game.
T2: The Arcade Game: Aside from the game that was based on the movie that no one wanted to play, courtesy of LJN, the better game was the port of Midway's Terminator 2: Judgment Day arcade game. The Genesis game was much more fun to play, and was one of the few games that would work with the Menacer. The SNES game was plagued. Despite having light gun support, allowing it to work with the Super Scope, when this was used, the background would become bright blue, rather than the dark future scene that the movie shows us. More importantly, Arnold's most famous line, "I'll be back," was absent from the SNES version for some reason. Why?