I wouldn't mind (and I think I'm sort of alone here) a complete three or four film series set entirely in the past... and then 'kill' them or whatever and they could disappear and be brought back at some point 20 years from now or as appropriate.
Of course the problem with that is we want to see Hulk/Thing, Torch/Spidey etc. And, of course, we need to see Dr. Doom taking on everybody - but Doom, as has been mentioned, might be able to cross-over a lot easier.
And that element would be sort of cool - establishing Doom as the ultimate bad-guy in the past then have him popping up to threaten a world that thought they were done with him.