To me there is no issue, only people who are making an issue by questioning it all. Read Agent 194's post. He's absolutely right, if they just come out and have Iron Man, the Hulk, Captain America and Thor standing side by side and just being the Avengers as they've been for years in print, never questioning Thor's magical roots, Banner's gamma radiation anomaly and Captain America's real chances of surviving that long in the ice. They do that, and nobody but those already skeptical will think twice.
You ever hear about Harry Potter? They're these stories set in the modern day about a school for wizardry. They've been quite successful movies from what I've seen.