If Peter Parker's story is truly coming to an end (it's probably not) the biggest unresolved question won't be who he ends up with, but whether he'll ever find out about what happened in One More Day. Fans have different opinions on whether he should remember.
There are two elements to the question. What should happen if Peter Parker's story is actually going to come to an end? What should they do, under the assumption that the story will continue?
Tom Brevoort was asked about this on his formspring. His response is in bold.
My problem with OMD is that there isn't any lasting drama because no one remembers anything. Making peter the only one who remembers would have make everything far more interesting. Did you consider having peter be aware of the change? (or is he?)\
He isn't, nor can he be, really for the same reason that the "fake priest" idea doesn't work: if Peter is aware of who things have changed, then shouldn't he be devoting all of his time and energy to getting back what he lost, restoring his marriage? That puts you right onto a storytelling treadmill from which there's no good escape other than simply going back to the old status quo.One More Day is convoluted. Technically, it's not a matter of memory, as this Peter Parker never was married. The marriage was an alternate timeline. Any story in which Peter learns about the deal with Mephisto would have to take that into account. There would also have to be some sort of explanation about how Peter Parker came upon this information. Although, with Madame Web as a supporting character, there are various opportunities for writers to give Spider-Man insights into things that require cosmic awareness.
One question after One More Day was whether it had actually been a matter of memory rather than time travel. So I'll address the implications of that. It does seem a bit more satisfying to readers, as it means that everything in the earlier comics still happened, even if characters don't remember it. It's not a retcon, as the stuff actually happened just the way it was depicted as happening. Characters just remembered it differently.
Although there is an uncomfortable subtext. If this Peter Parker and Mary Jane are actually married, and just don't know it, that raises some thorny questions about adultery in any future relationship. And it would be too easy to just reverse everything, and restore the earlier status quo.