Here's how I'd handle the future of the franchise
Now if Fox is smart, they'll set Apocalypse in 1986 or 1988 as that's when his first appearance was as well as Fall of the Mutants. There were so many cool X-Men characters and concepts introduced throughout the 90s along with some great costume redesigns (about the only part of 90s Marvel that was good aside from Peter David Hulk and the work on Iron Man by both Len Kaminski and Kurt Busiek) that the rest of the franchise along with Fantastic Four should take place from then to the early-mid 2000s. Mostly since it's hard to imagine those uniforms being stylish by today's standards. X-Men is a VERY 90s franchise and there's nothing wrong with that but it kind of is.
Anyway, here's how I'd progress the series after Apocalypse
Part 1: X-Men: X-Cutioner's Song. Set in the early 1990s with most characters wearing Jim Lee uniforms. Stryfe and Apocalypse are the main villains initially while Sinister plays everyone against each other. By the end, Sinister gives Stryfe the Legacy Virus as a last ditch to kill Apocalypse with. In this continuity, the Legacy Virus works like HPV in the sense that humans can't die from it but mutants can in the same way that men pass on HPV to women but it has no effect on males. Sinister reveals himself as the true villain after Stryfe is completely bested by Apocalypse and manages to kill him.
Part 2: X-Men: Messiah Complex comes next. This is where Sinister gets his chance to shine as the big bad, revealing that he's responsible for Weapon X, tying him to both Wolverine and Domino (and possibly Fantomex if he's been introduced by this point in time), collaborated with Sebastian Shaw to the point where he's the one who encouraged Xavier and Magneto to meet up by giving Magneto the tips to lead to Shaw's yacht, worked in genetics with Xavier prior to forming the X-Men, ran Cyclops' orphanage and was the mysterious benefactor that led Jean Grey to the X-Men. Moreover, Gambit was spying for him all along. And Magneto's first encounter with Shaw was when he was infiltrating the Nazis for British intelligence during World War II and managed to get inside Auschwitz, in fact, he's the reason why Shaw spared Magneto in the first place.
Sinister decides that the X-Men have outlived their usefulness after Apocalypse died and cannot allow them to recruit a child detected by Cerebro who may be the most powerful mutant ever born. Without Apocalypse to threaten him, the Marauders should be the only mutant faction allowed to operate as the X-Men merely complicate his plans for world domination where mutants become the dominant species who must accelerate their destiny to replace humanity by whatever means necessary.
Then Bishop enters the picture at first pretending to assist the X-Men but really planning on double crossing everyone as Sinister getting his hands on the child was the catalyst for the sentinels being given orders to eradicate all of mutantkind in the first place and he needs to murder her to ensure that the events Wolverine went back in time to stop would never happen. Gambit naturally betrays Sinister and assists the X-Men, effectively taking Bishop's place in the team. Eventually, while the X-Men fight and eventually kill Sinister, Cable takes the girl across time where she'll be safe until she's old enough for her powers to activate. Bishop follows cable, determined to stop him.
Part 3: X-Men: The Phalanx Covenant. This would be more of a mashup of Welcome to Genosha, X-Tinction Agenda, Phalanx Covenant and Second Coming with a pinch of Operation Zero Tolerance than a direct Phalanx covenant storyline.
Cable returns three years later with the child, now 15 or 16 years old. In this time, Wolverine has been leading X-Force in his place. Anyway, The Island of Genosha elected their first mutant Prime Minister which lead to a military coup by General Cameron Hodge. Hodge has proceeded to round up mutants to serve as a slave underclass that has effectively turned Genosha into an economic superpower with enough wealth to evade sanctions without significantly harming the interest of any nation willing to take action. After returning from the future, Hodge kidnaps Hope Summers and plans on using her as a weapon to hunt down and capture/kill other mutants (fulfilling the role of Wolfsbane and Havok in the comics). After the first wave of X-Men arrive, they find themselves kidnapped and forced into servitude with one even being implied to have been raped. Wolverine escapes but his healing factor is gone, causing the adamantium in his bones to be slowly poisoning him. Assuming that Archangel isn't transformed by Apocalypse earlier in the series, he certainly gets transformed now.
Hodge eventually hears from his head scientist Sebastian Gilberti, leader of the Bastion Initiative (and himself secretly an android who's the remnants of the original Sentinel project that uploaded himself to the proto-internet back in the 1970s) that work on Project Phalanx is going according to plan as a nanotech virus that will grant it's users superhuman powers without having to rely on genteics. It's even progressed to the point where a being made entirely out of circuitry named Warlock has already been created. Warlock is unsure of his role in this and questions why his existence means that mutantkind must be destroyed, openly stating that Genosha's military still uses obsolete technology to perform many tasks. After the second wave of X-Men land, Hodge and Bastion decide that the time is right to commence Operation Zero Tolerance, which involves eliminating all Genoshan slaves before they can successfully overthrow the government. Cemeron Hodge after being injured in an assassination attempt by Magneto decides that the only way to stop the X-Men who are currently revolting is to inject himself with Phalanx despite it never being tested before on a human host (outside of Bastion but he's already a machine and is obviously lying to Hodge about there being side-effects). Hodge begins healing himself and realizes that he now has the power to shape-shift and is an organic computer. He goes mad from his newfound power and begins infecting his own people with the virus, transforming them into a hive mind with Hodge as the controlling intelligence. Bastion however begins to view Hodge as a rival as he goes progressively crazier and orders the Sentinels that he was secretly building to control the Phalanx and moreover, to subjugate the humans to his will and kill any who resist.
After encountering Storm who overcharges his circuitry, Hodge begins transforming into a hideous cybernetic monstrosity that begins consuming all organic matter around him but retaining his human head. As he goes from a spider/snake creature into eventually just a giant blob, Cyclops manages to kill him alongside Cable.
Meanwhile Hope is rescued and returned to normal by of all people... BISHOP who may have been hunting her through time but realizes that she's now mutantkind's only hope of salvation. Bishop offers to help join the X-Men and atone but he needs her to rejoin and free the X-Men from Genoshan control along with killing Bastion.
After defeating Bastion with Hope enhancing everyone's powers, the X-Men destroy the citadel where mutants are processed and Magneto stays behind to be the new leader of Genosha. ANd at some point, Warlock should sacrifice himself to save one of the X-Men.
Part 4: X-Men: Fatal Attractions. This is more of a mashup of Mutant Genesis, Magneto War, I, Magneto, Eve of Destruction and Fatal Attractions where the Genoshan Magistrates are renamed the Acolytes and Tam Anderson is sharing power with Fabian Cortez who Magneto trusts more as he's a mutant and suffered under the regime, unlike Anderson who was openly served Hodge. Little does Magneto know that Cortez is feeding him information saying that the world is planning to assault Genosha because they fear a nation not just led by a mutant but Magneto, whose actions in the 60s and 70s have caused the world to see him as a threat and are preparing a nuclear strike.
Magneto naturally offers the world one week to completely disarm all military stockpiles and hand the world over to him completely. Failure to comply will result the Acolytes devastating major cities across the globe. Once the United Nations activates what they term the Magneto Protocols, Magneto orders the city of Varykino, Russia destroyed. With millions dead, the United States tasks the X-Men with invading not only Genosha once again but also the space station that Magneto has retreated to called Avalon.
Upon reaching Avalon, Cortez encounters Colossus who is confronted with the evidence of the Magneto Protocols existing and Russia's attempted nuclear strike on Genosha. This X-Man defects and Magneto is forced to serve the X-Men. Magneto rips the adamantium out of Wolverine's skeleton after Wolverine tries to assassinate him but is kind enough to leave him recovering in an infirmary.
Eventually, Magneto morally wounds young Hope Summers and begins to retreat from battle where he confronts Cortez who is being held hostage by Tam Anderson. Cortez admits that he was feeding Magneto faulty intel for years in the hops of Magneto starting a war to exterminate humanity for the pain that the Genoshan Magistrates caused him and just to prove how serious he is, he murders Tam Anderson right in front of Magneto and escape to Avalon's control room.
Xavier using Cerebro communicates with Jean and requests that the two of them band together to wipe Magneto's memories in the hope of forcing him into a peace treaty, failing to realize that Cortez is the real enemy. After confronting Magneto wrestling with Cortez, Jean sees that the X-Men were already too late, their mission was a sham and the Magneto Protocols were activated, causing Genosha to be wiped from the face of the Earth by nuclear bombardment.
Jean breaks down after realizing the peace between humans and mutants has now been made impossible. She and Xavier agree to mind-wipe Magneto while Cortez thanks them and then activates Avalon's self destruct and then takes an escape pod down to Earth.
Realizing too late that Cortez was their true enemy and he's successfully escaped,The X-Men take the wounded Wolverine and Hope along with the unconscious Magneto with them back to Earth and escape with the surviving Acolytes. Xavier and Jean while inside Magneto's mind relived Magneto's memories within an instant and realize the hard way that Magneto had a point to everything he did and vow to restore him within the X-Mansion. Magneto, having come back to his old self again now looks at Xavier and asks if it's truly wrong to want to hunt down and kill Cortez. Xavier says that he'll allow Magneto's vengeance to take place.
Post credits, Cortez is seen on the run and encounters the shape of Magneto hiding in the shadows. Cortez acts shocked and simply says, "you!" before the screen fades to black and we hear a scream along with some truly gruesome sound effects.
Part 5: X-Men Onslaught. Bishop recalls the current date on the calender from the future of the current timeline back when he was chasing Cable. One of the X-Men will indeed betray the team and leave only Gambit remaining. All of the X-Men deny that it could be them. Bishop points out that Gambit being the only survivor and refusing to tell Bishop who it was makes him the obvious suspect, not to mention his past spying on the X-Men for the Marauders and he's forced into quarantine. Naturally, there's the possibility that somebody else may have been the traitor and everyone remembers what Bishop did back when he was hunting down a small child. Bishop replies that it may be Hope Summers as she's the reason why his original timeline was destroyed. And even then, everyone admits that Wolverine has a shady past, Colossus just betrayed them, Rogue used to work for Mystique and Magneto is their oldest enemy.
Things aren't helped along when Magneto appears on some security cameras massacring an anti-mutant lobbying group called the Friends of Humanity, which Magneto denies. Xavier mentions how Magneto recently attempted to murder Cameron Hodge in cold blood and recently hunted down and killed Fabian Cortez. Magneto also denies killing Cortez, nor for lack of trying but because somebody else beat him to it.
The X-Men now know what they have to do. Mystique is involved and they need to know why. Mystique has no idea why Cyclops is blaming her for anything as she's given up a life of crime and now leads a government-run mutant team. She's not guilty of anything, nor has she been trying to frame Magneto. If anything, she saw the footage and was prepared to attack the X-Men because she believed that Magento did it, despite his alibi and people seeing him in the X-Mansion on the same day.
Returning to the mansion with Mystique in tow, the X-Men, X-Force and Mystique's team X-Factor along with the Reed Richards of the Fantastic Four are told by Bishop that today is the day when it happens. One of them is indeed going to murder the rest. An alarm rings as Gambit has broken himself out of captivity. The team is disorganized and Gambit runs into Bishop while attempting to break out of the X-mansion. Gambit tells Bishop right to his face that he knows how to find out who's guilty based on the footsteps he heard around the mansion and who was walking where. Whoever is about to betray the X-Men is going to walk into the Cerebro chamber, where he heard a lot of new equipment being moved over the past few days and to head to the security room and watch the cameras. As Gambit and Bishop check the security feed they see
Spoiler!!! Click to Read!:
Professor Xavier in the Cerebro Chamber.
Xavier puts on Cerebro as Gambit says that they can't believe that Xavier of all people would be working against the team he founded.
Spoiler!!! Click to Read!:
Another figure approaches Xavier. It's Magneto. Xavier asks why Magneto is here, Magneto proceeds to kill Xavier in the exact same way that Cyclops did in AvX under the power of the Phoenix Force. Magneto then turns to face the camera and we see the face of
Spoiler!!! Click to Read!:
Jean Grey. Having absorbed Magneto's memories aboard Avalon and seen the destruction of Genosha firsthand, Jean gave up on Xavier's Dream and now seeks to destroy all mutants and humans alike. She gazes upon the camera and says, "I know you're there Remy. You wanted to see an onslaught, well I AM ONSLAUGHT!"
At this point, the X-Men, Fantastic Four, X-Force and X-Factor combine their powers to stop Jean who's now donned the uniform of the Dark Phoenix and admits that she wishes to destroy the entire world, mutant and human alike. she immediately murders everyone but Cyclops and Wolverine and mentions that she's currently using her psychic powers to slaughter entire continents. Wolverine then attacks stabs Jean multiple times but she also reduces him to dust.
Cyclops pleads with Jean to stop as she's just killed off an entire world but then, a small child climbs out of the Fantastic Four's vehicle and asks her if she wants to hurt him. Jean stares into Franklin's eyes and says, "yes." Franklin asks her why and Jean has no reply. She's bothered by Franklin's innocence. Franklin says that he's a telepath too and know what she's been doing. He's been transporting everyone she's killed to a "counter Earth" where she's never turned bad. Cyclops, as one of the three people alive asks if he can go there as one of the last three people alive. Franklin says yes and when asked what it's like by Jean Franklin says, "exactly like this one, but she never turned bad" and as they fade he continues, "and we're in charge"
Part Six: House of M (Not even truly an X-men film, an X-Men/Fantastic Four crossover)
This one ends with Franklin creating yet another world but says, "no more mutants." We all know how that turns out.