I think the OT will eventually play itself out coming off the changes made in 1973, but it will be a slightly different variation of the OT. I don't think you can change Stryker or Jean's fates because that would undo X2 and X3 entirely. I still think we are stuck with that version of the Phoenix for now, but a different incarnation could always appear later on.
Honestly, the Cyclops thing, I think he will be written back in if Singer is gungho about providing fan service. I could see the future scenes where the X-Men are outgunned, but Cyclops comes back as a last minute reveal. We have a three year gap from The Wolverine after credit scene and TLS, and another seven years until DoFP (future). That means there is plenty of time to explain Cyke's possible whereabouts. Considering the future is only supposed to be an action packed 45-50 minutes or so, I can see them slipping Marsden in at some point.
Outside of that, I don't think the fans have too many problems with the current narrative and the way things played out in the OT.
I don't even know if we're gonna get that much, that's like half the movie almost. But I'd love it if that were the case.
I don't know what they are gonna do with potential timelines. I have a few theories.
The main, prevailing one, is:
X-Men: First Class -> X-Men Origins: Wolverine -> X-Men -> X2 -> X-Men: The Last Stand -> The Wolverine are all a singular timeline, and it is this timeline that leads to the future of X-Men: Days Of Future Past. So the future portions of the film are all within the same timeline as the previous 6 movies.
So from there, we have the time travel back to 1973. The comic book storyline of Days Of Future Past has Kitty Pryde returning to the future, and nothing has changed. But I believe the time travel now has 2 main possibilities:
1.) The time travel exists in the above listed timeline, meaning the events of Wolverine traveling to the past, meeting Xavier and Magneto, and whatever happens in 1973, is all part of the timeline. It won't actually undo or change a single thing, because this is what always happened in the timeline to begin with. The Xavier and Magneto that we see in X-Men met Logan in 1973 and experienced whatever it is they will experience in the movie, and this is what always happened. But it will also mean that the bleak, apocalyptic future will always happen, as that's what's meant to happen. Nothing can be nor will be changed. This theory presents the timeline as follows:
X-Men: First Class (1944-1963) -> X-Men: Days Of Future Past (1973) -> X-Men Origins: Wolverine (1975-1981) -> X-Men (2013) -> X2 (2013) -> X-Men: The Last Stand (2013) -> The Wolverine (2014-2016) -> X-Men: Days Of Future Past (2023)
Future First Class movies will fit in on that timeline anywhere between X-Men: Days Of Future Past and X-Men (1973-2013), and the possibility exists for future main trilogy cast X-Men films taking place in or after this bleak future.
2.) The original timeline of the 6 movies remains the same, leading to the events of 2023 Days Of Future Past. However, the time travel events of Days Of Future Past -aren't- part of the natural history of the timeline - I.E.: The Xavier and Magneto that we met in X-Men never met Logan, he had never time traveled in time yet, and the time travel will change the events of 1973. This adds many different options.
a. Logan traveling back in time is obviously a new development for the time frame as we know it, and doesn't necessarily need to match up with Xavier and Magneto not knowing Logan in X-Men, because they wouldn't have until 2023 came along and Logan had to be sent in time. But the events of X-Men: Days Of Future Past do change the events that lead up to the Sentinel takeover, and it never happens. However, outside of that, that's the only real change that's made. The Sentinel takeover never happens, but the rest of the timeline plays out the same way. This timeline looks as follows:
X-Men: First Class -> X-Men Origins: Wolverine -> X-Men -> X2 -> X-Men: The Last Stand -> The Wolverine -> X-Men: Days Of Future Past (2023) -> X-Men: Days Of Future Past (1973) -> New Days Of Future Past future (2023)
b. Logan traveling back in time does create a new timeline. The original timeline exists all the same, but now instead of the events of 1973 leading into the main trilogy, and everything else playing out the same, a new timeline is created, and there are 2 parallel timelines that branch off of each other at the events of 1973. That leaves the timeline looking like this:
X-Men: First Class -> X-Men Origins: Wolverine -> X-Men -> X2 -> X-Men: The Last Stand -> The Wolverine -> X-Men: Days Of Future Past (2023) -> X-Men: Days Of Future Past (1973) -> X-Men: First Class (future sequels / continuation of new cast and timeline)