Guys I have a theory or something
I think Marvel could structure the Mutant Saga somewhat like the Infinity Saga, with different characters filling similar narrative roles:
Mr. Sinister could be the Loki of the Mutant Saga: a recurring villain who manipulates things from the shadows, with his obsession with mutant genetics, the Summers family and Jean giving him plenty of material from the comics.
Apocalypse would be the Thanos of the saga: the bigger threat whose presence is slowly built up across multiple movies before becoming the main villain.
Jean, Cyclops and Storm could be the Tony, Cap and Thor of the Mutant Saga — three of the main pillars of the X-Men, each representing a different aspect of the team.
Wolverine could be the Spider-Man equivalent: the most famous mutant, with his own solo saga that occasionally crosses over with the main X-Men story.
And Stryfe could fill the role of the Infinity Stones, or at least the equivalent of the ultimate MacGuffin that the final villain is trying to obtain. His comic history already connects him to Apocalypse, Cable and Sinister. Apocalypse infected Nathan Summers with the techno-organic virus, Nathan was sent into the future, and a clone was created as a backup. That clone eventually became Stryfe and was raised by Apocalypse's forces.
So you could have Sinister's experiments leading to Cable's creation, Apocalypse wanting Cable/Stryfe for his own plans, Stryfe becoming Cable's archenemy, and all of those threads eventually converging in the Apocalypse storyline.
You could even incorporate the Legacy Virus, since Stryfe's comic history is connected to that as well.
Basically, the Mutant Saga could have its own version of the Infinity Saga's interconnected storytelling without just copying the MCU, because a lot of these connections already exist in the comics.