I've never been bothered by the facades, IMO if it was more realistic, it would look like New York over in Studios, I think the comic bookiness suits it. I would like to see an update to some of the character shots/costumes around the area, but not necessarily the "film" versions. Some new characters and "shows" would be nice, if that's possible. I would love to see some Shield agents (not from the show please!) fight it out with Hydra or AIM and losing the hero trike parade (that feels straight out of the x-men cartoon) would be a plus. More X-Men, some FF,some Avenger meet and greets. I mean Iron Man would seem to be fairly easy if they can use him.
With the right story and system the dark ride could be a blast! Tie it in with new characters and street shows, m&g's. I'm not really sure about using anything from Gringotts though, or any other ride profile for that matter. Like it or not, IOA and USF are really being enjoyed as one large park, if too many of the rides are similar (especially the E-tickets) that would get old real quick. C & D's can be similar, but the E's really shouldn't be.