For what it's worth, the more that I play mixed-universe games, the more I find that the disparity in power between Marvel & DC at the higher level characters gets more difficult to reconcile if you're using a numerical stat system. Heavyweights in the Marvel Universe just can't stack up to their DC counterparts. Thor, Hulk, and Juggernaut all top out around 100 tons of lifting, while Superman, Doomsday, and Wonder Woman surpass that by orders of magnitude. There's only been 1 time that I can think of when a Marvel character displayed DC-level strength, and that was in Secret Wars where the Hulk held up a mountain to keep himself and his companions from being crushed after it was dropped on them.
Yes, most of the times, the strength/power comparisons get handwaved in the comics, especially in the Marvel Vs. DC fights, but that's because the characters so rarely interact. On a MU, you have these characters interacting much more regularly, even if you only do 1 or 2 crossover events a year.
I'm probably in the minority, but I'm fairly burned out on FC super games. A lot of this has to deal with the heavy competition for the big name characters. With OC games, you can create obvious homages, but at least they're your character(s) and you can bring them to life without relying on previous comics canon, current comics storylines, or having to ret-con what a previous player may have done. You're also more free to write your own character without having to worry about how it might affect the prospect of a future player picking the character up at a later date.