Ok, here is an idea...
The side missions would expand this game in a way most people could have never dream of... BUT what do you think about this...
Instead of making side missions for a specific character (Colossus/Wolvie/Cyclops)...
WHY NOT MAKING THEM FOR A SPECIFIC TEAM?Imagine in EACH act (posibly excluding the last act so that the MAIN battle doesn't loose interest) a side mission for a specific Marvel Team.
Examples:
Fantastic Four - If you are playing with this team, you could have side missions with the following mini-bosses:
Dragon Man - Already in game as villain.
- Stage could be the jungle in XML2
Gladiator - Already in game as villain.
- don't know which stage...
Doc Doom - not in act 4 nor 5 since it's closer to the final battle
- Doesn't matter which stage... Doom is all we need

- He's the MAIN villain, maybe not a good char for a side mission...
SuperSkrull - Same as Dragon Man, already in-game
- no idea which stage XD
That pretty much makes 4... 1 for each of the 1st 4 acts... The good thing about using chars that are already "in-game" as villains would be to make the mod have better quality and at the same time, don't need to add new stuff...
Same could happen with other groups, like Xmen or Avengers...
X-men - as long as you have all Xmen chars in your group you could face
Brotherhood (a small gang of mini-bosses would be cool... Blob, Avalanche, Pyro and Toad), Magneto, Omega Red, Centinels, or even Apocalypse.
Avengers - as long as you have all Avengers chars in your group you could face:
Wrecking Crew, Destroyer, Kurse, Radioactiveman... you get the idea
I don't know... just throwing the first villains that come to mind, but you guys get the idea.
I think it would be much better to do it with groups, instead of specific chars. This would allow for more "customization"... since you still can choose WHICH of the members of that group to take... and not just take Colossus to do the side mission if you don't like the guy.
Just a thought... let me know what you guys think about it...
Cheers, and GREAT IDEA!!!