A total canon reboot sounds like the easiest and most interesting way to go. A lot has happened in both comic and MM canon that I think could easily be stripped away without losing anything in a new game.
I love DC, but am not in favor of seeing it mixed up in a Marvel game. I think it would be too hard to execute without being total crack.
To be honest, I am not at all an Avengers fan, so it would be hard for me to get into an Avengers only game. If you kept is two small teams... a small group of Avengers and a small group of X-Men, that could work. I kind of like the idea of having separate comms for each team.