As with most entries of the Marvel vs. Capcom series, the entire OST qualifies. While many will agree that the original music for the characters who didn't have their usual Leitmotifs carried over lacked the staying power of said themes, virtually no one would ever say that the compositions weren't damned catchy.
Porting Disaster: The PS1 port omitted the tag team gameplay due to the system's limitations. Nothing new as X-Men vs. Street Fighter did so too. The faster gameplay and extra color schemes more then made up for it and there's a somewhat limited version of the tag team included.
Sequelitis: Most serious players find the game to be stale and boring due to all the nerfs and balancing done to the game in reaction to the sheer insanity of the previous game. Also, despite all this, Wolverine is still broken. That said, the game maintains a respectable following overall. It wasn't until the sequel did said sheer insanity return.
Squick: One of Norimaro's planned attacks for the Japanese version had him fantasizing about a certain Capcom character and spouting a nosebleed. Two of these characters were Anita from Darkstalkers (a young girl) and... Zangief.