Joe & Mac: Caveman Ninja/YMMV

Polished Port: The Super NES version. It expanded the length of many levels, the music was superior to the arcade, the map screen was interactive, and it featured bonus rounds that the arcade version lacked. Its only downside was a lower framerate than the arcade.
Porting Disaster: The SNES version of the game did get expanded levels, sprites directly derived from the Arcade Game, and a lush color palette... But it removed elements like charged weapons, interacting with your co-op partner (a mode which is unlocked after beating the game), and (worst of all) suffered from sluggish controls and a drastically reduced frame rate that seemed to run at half the speed of its Sega Genesis counterpart. On that note, the Genesis version lacked two weapons from the arcade version and fell victim to the system's notoriously stingy color palette, but included nearly everything else and even ran faster than the arcade version for added challenge.
That One Boss: The dinosaur skeleton in level 10. The fight itself is fairly easy, but for the first half of the fight, instead of displaying a hurt animation, the skeleton just breaks apart and showers the screen in bones in an attack that's nigh-impossible to dodge, and can very easily just turn into the player and boss trading hits (and since the boss has more health than you, you'll die at least once).