In my view, people are overthinking the problem... and it's something that will actually get better as time moves forward, not worse. How?
An example is in how Captain America is cited as a man out of time, who eventually will be stretched to the breaking point as WWII becomes a distant memory.
But let's turn it into a parallel example. Let's say that instead of Captain America, we're talking about, oh, Captain Sparta. This guy who's a frozen Spartan warrior thawed out in whatever year. No matter if he appears in 2011, or Space Year 2511, the foundations of his character and what he represents will resonate, because the story of his era - romans and spartans and greeks and persians - has become a solid historical and mythological foundation.
It's weird that some folks don't see events like World War II have achieved the same kind of transcendent historical positioning. People aren't going to forget what kind of characterization WWII gave to the world of its era; it's going to remain a studied subject of history. It's iconic. If WWII being distant was enough to break Captain America, it would have already happened by now - 40s and 50s America is dead and buried (in spite of one last gasp of a real world political movement to bring the worst parts of it back from the dead). Kids today with thar cell phones and thar facebooks and thar internet global community awareness shouldn't have any reason to identify with Captain America, yet they do. People still get what the guy stands for and why he can be poignant, when written well at least.
Eventually, Cap (as just one example here) will indeed become more mythological, like a frozen man of Sparta out of time, but that won't ruin the character. He might become a little more like that partial tribute to him, The Old Soldier from Astro City. But if anything that'll just allow the character to become a more powerful figure. (Heck, I'd go full retro, and emphasize Cap's World War II origin with his presentation and dress.)
Same thing applies to Magneto and Xavier, really. It's just that Xavier hasn't been treated quite as mythologically as Magneto, so his position is a bit more strained. That can be fixed though. Xavier and Magneto eventually, should perhaps become two legendary figures from the mists of time, who inspire a kind of awe when they reappear.
In fact, one of the major plot threads of the 90's X-men relaunch was that Magneto's DNA was tampered with by Moira Mctaggert, making him more docile (and hence joining the X-men for a while in the 80s).
