While the censorship certainly hurt sales, with the SNES version selling 1/4 of what the Genesis version sold, the port was bad for reasons beyond the censorship. The sound and graphics (aside from the blood and gore) were spot-on, but the game itself was very buggy. The combos were broken due to lag, and when two players threw projectiles at each other, when the first projectile hit, both disappeared. Not only did that look bad, but MK's designers deliberately wanted projectiles to pass through each other as opposed to Street Fighter, where projectiles canceled each other out. One of the fun things in the arcade was having two Sub-Zeros freezing each other and then having one player try to be fast enough to where they would thaw out sooner and be able to go in for the kill. The Genesis version didn't have these bugs and played a lot better than the SNES version. According to Ed Boon, the issue was apparently that the SNES couldn't handle both making the characters big on the screen and good hit detection at the same time. The character sprites in MK2 were somewhat smaller on the SNES, and the game played a lot better.
Despite the fact that MK was one of the main motivations behind the creation of the industry-wide ESRB ratings system, MK2 came out on the SNES and Genesis exactly one week before the ESRB ratings system went live. Nintendo put its own content warning label on the front of the SNES MK2 box.