The endings have gone back to sprites instead of pictures, a method which was last seen in X-Men Children of the Atom. The hidden Marvel characters (Mega War Machine, Orange Hulk and Red Venom) have just got the same "You beat the game with a hidden character" ending, so I haven't bothered covering those. Onslaught can be used in the console versions of the game, but beating the game with him just gets you the same ending the hidden Marvel characters have.
Mega Man's ending is a parody of what happens when you beat a boss in most of the 2D Mega Man games. The game Morrigan and Ryu start to play in Morrigan's ending is Super Puzzle Fighter II Turbo, which was another game Capcom had released in 1996. Strider Hiryu's ending is more or less the exact same ending in the original Strider arcade game. Captain Commando's ending is also similar to the ending from Captain Commando.
Spider-Man's ending will have him take a picture with whoever his partner character was -it just happened to be Morrigan when I beat the game with him. The same goes with Venom's ending -I just happened to have Wolverine as the second character when I beat the game with Venom.