What makes X_Men different if with exception of Loki and Scarecrow villains don't come back.
Let's remember that because the trilogy was erased by time travel we have never had Magneto VS X-men In films now.
First of all, Stryker is a reoccurring villain.
Second point isn't entirely correct either. They still left that open. What we don't have is Wolverine and the X-Men as we knew it in the OT. Whether Wolverine joins the X-Men after Apocalypse or not is irrelevant. We don't have the adamantium and Weapons X in the way it was portrayed. We don't have Wolverine and Rogue in X-1 meeting the X-Men because Charles/Hank will have known Wolverine all that time, given his new connection with the X-Men and Mystique in 1973.
However, Magneto could still hatch his plan to convert participants in the UN summit into mutants. You could also have Stryker kidnapping Xavier and hatching his X-2 plot. He just wouldn't have the history he did with Wolverine. Jean could still DIE at Alkali Lake. We can't assume Xavier is omnipresent and will be able to prevent everything. We can also assume the government still tries to weaponize The Cure, or some form of it.
The only way to fully swipe the OT is to ensure Magneto has a complete change in philosophy than that which dictated his methods from the OT, by no longer instigating the war. The perfect way to do this is Age of Apocalypse. Kill off Xavier or have him severely debilitated, have Beast become the leader along with Magneto (albeit temporarily). Magneto can be written out or pursue his own ambitions following the events of Apocalypse.
Age of Apocalypse would be my primary inspiration and a good way to conclude the Xavier/Magneto arc. I don't think they will kill off any of the FC actors however, but it's a perfect way to thematically conclude the story started from FC.
Edit: Well, they couldn't kill Jean/Xavier given the ending in DoFP, assuming Apocalypse is the same timeline as that. But there are still ways to capture AoA thematically without doing that.