The one where Apocalypse was the boss? How about Spider-Man/X-Men? The one with Arcade.
Heh, well I played Children of the Atom by Capcom so many times as Omega Red and Silver Samurai, I can truly say that Wolverine, Iceman and Magneto were cheap scrubs.
No. In 1990, I think Konami or Acclaim made a beat-em-up X-MEN arcade game based on the character models from the 1989 pilot, PRYDE OF THE X-MEN. Normal machines allowed for 4 players, jumbo ones for the full 6. You chose between Cyclops, Wolverine, Colossus, Nightcrawler, Storm, or Dazzler across about 4 or so levels, fighting Magneto's hordes of Sentinal robots and other various creatures, and his Brotherhood, to rescue the kidnapped Xavier & Kitty. It's simple and dopey, but I played the hell out of it as a kid. It was never ported to a home system.
Sega made a Spider-Man themed beat-em-up in 1993 I believe, which featured as other characters to choose from Black Cat, Hawkeye, and...Namor. Yes, very random. That thing was F'ing hard. I'm the only person I know who drained enough quarters to beat the damn thing.
The only 90's Marvel beat-em-up that saw a home consule release was AVENGERS, which wasn't that hot, but the marble-mouth voice acting is half the fun.
"Fwank Ooo, Washp!"... "Amerwica stwill needs ywur HELP!" Hilarious. Plus, Crossbones was a boss.