While we may say that X-Men: Days of Future Past completely erased the movies from the original X-Men trilogy, this isn't necessarily so. More than once in that movie, it was explained that traveling back in time will change the history as we know it - but it won't change it completely. In a sense, time is immutable and what is meant to happen will happen.
So, as Simon Kinberg explains, "the point is, time's immutability. The idea that time is like a river. You can splash it and mess it up and throw rocks in it and shatter it but it eventually kind of coalesces and this is, again, theories of quantum physics. It's all based in quantum physics." So now the question is not if, for example, Stryker is the one to experiment and bond Wolverine's bones with adamantium. The question is when will someone do this to Wolverine (is it Mystique, or Apocalypse himself to do that?)
And this is the reason why the following spin-offs won't be set in the original timeline, but in the post-Apocalypse one (even if much later on). For example, in the original timeline as well as in this altered one, Deadpool is still a part of the Weapon X program. But while in the original one he had his mouth sewn, in this new one it won't happen in the same way.
Read More: How Does Deadpool Fit Into the MCU Timeline?
This can also be said about Gambit, who ran away after being in the Weapon X program - now he will do that for another reason. And we suspect that someone will experiment on him too, namely Mister Sinister (who himself is a creation of Apocalypse and, thus, a new character).
This whole time-related theory is pretty interesting, as well as pretty beneficial for the whole X-Men franchise. And that is because this gives the studio the chance to tell stories from different perspectives, with the same or with new characters (for example, Bryan Singer already said that he might take on the task of adapting the Dark Phoenix Saga).
Returning to Days of Future Past, the ending revealed that Wolverine finally had some closure, Scott and Jean didn't die, Professor X was alive as well, and so on. And this might be some sort of happy-ending which is already established. And, if we are to believe Kinberg, this is the ending for all the X-Men franchises. But it needn't be so, as Bryan Singer explains.
The waking of Apocalypse won't just change the smaller details in the timeline - it can also alter this outcome. Some heroes might die, while some other might live. Old characters might return, while some newer ones might be added: "So, yes, that is the outcome we hope for. That is the outcome we aspire to and that's the outcome we are moving towards, but we saw in Days of Future Past another dark world. What says that can't happen again? What says the awakening of a being that has such power and can acquire the power to destabilize that? So anything is possible. That's what we'd like to think happen, that's what Simon would like to think is a good outcome, but to me it's fair game."
And we believe that this doesn't just open the possibility of constantly rebooting the shared universe. It also brings the opportunity of telling stories outside of it, in parallel universes.
As said, Gambit, Deadpool, and Wolverine will take place in this post-Apocalypse timeline. But what that really means, especially for Wolverine whose third solo outing will bring the adaptation of Old Man Logan, is anybody's guess. That is why we believe that his story can take place in some other altered timeline, in which everything went wrong and in which Apocalypse was defeated at a greater cost. That is why we believe that the X-Men will be no more and that Wolverine was the one to bring their destruction.
There is no reason, however, to speculate at this moment, since the script for this later movie wasn't even finished. However, we can take from both Bryan Singer and Simon Kinberg the idea that everything can be changed, that the X-Men universe has expanded to all sorts of different other directions, some we haven't even thought about.
Via Screen Rant