I voted for Senator Kelly, Stryker, Lady Deathstrike, Callisto, Arclight, Psylocke, Silverfox, Agent Zero and Harada. Mostly since I'd like to see the new timeline take them to very different places.
Senator Kelly would find himself being urged away from using mutants as a scapegoat once they save his life and finds himself co-operating with Charles Xavier. He'd be a much bigger role in X-Factor where he mostly interacts with Valerie Cooper.
Stryker would retire from the military to become a preacher who leads an anti-mutant paramilitary group known as the Purifiers behind the scenes. Weapon X would instead by lead by Mister Sinister, John Sublime and Malcolm Colcord.
Lady Deathstrike would regain her consciousness and approach a wounded mercenary named Donald Pierce about a way to reconstruct his body using the adamantium bonding process. Together they form the Reavers and take the place of Gorgon and The Hand in the inevitable film adaptation of Enemy of the State where Deathstrike and Pierce use Wolverine's mental conditioning from Weapon X to use him as a Manchurian candidate against X-Factor which sets Wolverine on a journey to rediscover himself, starting with checking out abandoned Weapon X facilities.
Callisto would become an ally of Storm's after Storm challengers her for leadership of the Morlocks.
Arclight would join Weapon X instead of the Morlocks and find herself as part of Sinister's Weapon X special forces known as the Marauders. She'd still be little more than a cameo though.
Psylocke would leave the Morlocks to join X-Force and serve as the team's conscience.
Silverfox would survive and have Wolverine's healing factor implanted within her. She'd still be believed to be dead but crosses paths with Wolverine when they meet at the abandoned Alkelai Lake facility that X-Force already destroyed in X-Force 2 when they rescue X-23 and Fantomex from them. She takes the Place of Elektra in Enemy of the State as an assassin for hire. It turns out that Silverfox and Wolverine both have altered memories and they both remembered each other dying and they need to find out what happened, what didn't and only Lady Deathstrike may know the answers.
Agent Zero would show up before Enemy of the State in Madripoor in a loose adaptation of The Lazarus Project where he assists Wolverine and Karma in tracking down the carbonadium synthesizer so Omega Red doesn't release his death pheremones across the globe. Him being German instead of Asian-Canadian is retconned as being part of Wolverine's implanted memories. he gives Wolverine information that encourages Wolverine to investigate Weapon X in the first place after defeating Omega Red, although they part ways and he won't appear in Enemy of the State.
Harada would be the one transformed into the Silver Samurai after Ichiro Shingen dies but places a term in his will for Harada to become the defender of Clan Yashida at Mariko's command. He's now this tortured cyborg who still defends Mariko out of a sense of duty but he's overall a completely broken man now. I'd probably save him for after Enemy of the State.
I never cared for Toad, Mastermind, Quill, Wraith or Bolt and the films don't really need them. Viper was butchered because Fox didn't own the rights to HYDRA.
Also, the way I'd set up the Wolverine sequels is like this. The 2017 film is already somewhat confirmed to be Old Man Logan. I'd follow up with The Lazarus Project, then Enemy of the State, then Final Execution where Wolverine and X-23 fight Sabretooth and Daken, then go back to Japan to see how Wolverine's absence changed things with events unfolding very differently this time around. Shingen poisons Mariko, Silver Samurai blames Wolverine for her death and Ichiro was dead all along so nothing happened the same way and everything changes for the worse.
Plus, this means that Origins never happened and even the takes on the characters from that film were just bad dreams. It also means that Weapon X can also employ Truett Hudson, Abraham Cornelius, Sarah Kinney and Emrys Killebrew as their chief scientists and there will be a big enough Weapon X cast across Wolverine, Deadpool and X-Force films that they don't have to be introduced all at once but certain names will be dropped.
I'd also set up X-Force so that the first film takes place immediately before X-Men 7 in the early 90s. Genesis would be the big bad, the Dark Riders would be his goons, Sinsear would be a secondary antagonist and Stryfe would be the bad guy behind the scenes who lives to be the bad guy in X-Men 7. X-Force 2 would be an adaptation of Assault on Weapon Plus that would take place in the late 90s with John Sublime, Malcolm Colcord and Mister Sinister as the bad guys and Ultomaton and random Weapon X soldiers serving as the goons. This also keeps the events of X2 from occurring which is why Jean was still alive at the end of DOFP. It would also serve to bring X-23 and Fantomex onto X-Force and tease Mister Sinister as the big bad of X-Men 8 which would adapt Messiah Complex.
I'd also have the Fantastic Four series and X-Factor TV show be the future that the X-Men movies are building to. So when X-Men 10 hits, the timelines will merge perfectly and Old Man Logan would also be a preview of what happens by the time of our present.
This is how I'd build things
2015
Fantastic Four (2015, Doctor Doom as villain)
2016
Deadpool (late 70s, Ajax and Slayback as villains)
X-Men Apocalypse (80s, Apocalypse as villain)
2017
Wolverine: Old Man Logan (Specified as just "near future," Sabretooth as villain, first appearance of X-23, mostly a hint at things to come, particularly hints about the death of Wolverine's son. The Thing also appears.)
Fantastic Four: Annihilation (2017, Annihilus as villain)
2018
X-Force (1992, Genesis, Dark Riders and Sinsear as villains)
Silver Surfer (thousands of years ago, Reptyl as villain for first two acts, Galactus as villain for third)
2019
Deadpool 2 (1994, Juggernaut and Black Tom as villains, a younger Siryn pre-X-Factor also shows up)
X-Men: X-Cutioner's Song (1995, Stryfe as villain, Cable crosses over from X-Force)
2020
Wolverine: The Lazarus Project (1997, Omega Red as villain, Agent Zero and Karma first appear here.)
Fantastic Four: Revenge of Subterrania (2020, Mole Man as villain, homeless subway dwellers and moloids as goons)
X-Force: Assault on Weapon X (1998, Malcom Colcord and John Sublime as villlains, Mister Sinister as their director, Ultomaton as the big goon, Weapon X soldiers as other goons)
2021
X-Men: Messiah Complex (1999-2000 New Year, Mister Sinister, Sabretooth
and the Marauders as villains, Cable again crosses over from X-Force)
Deadpool 3 (2002, T-Ray as villain)
2022
X-Force: Phalanx Covenant (2005, Cameron Hodge as villain, Genoshan Magistrates as goons for first two acts, Phalanx as villain for third. Subtitle may be changed to X-Tinction Agenda or Second Coming.)
Fantastic Four: The Coming of Galactus (2022, Glactus and Silver Surfer as villains)
Wolverine: Enemy of the State (2007, Donald Pierce and Lady Deathstrike as villains, Silverfox as ally, X-Factor appear)
2023
X-Men: Fatal Attractions (2008, Magneto leads Genosha after it's overthrow at the hands of X-Force. However, his Defense Minister Fabian Cortez wishes to go to war against all of humanity and attempts to frame Magneto for attacks across the world in order to provoke Magneto into attempting world domination. The M-Men are sent in to investigate before the entire situation gets out of control. Magneto winds up mind-wiped, Genosha is destroyed ina nuclear strike, The Sentinel project is reactivated and Cortez flees the country. May also be retitled House of M.)
Deadpool 4 (2012, Garrison Kane as a Canadian government agent who wishes to bring Deadpool to justice)
Silver Surfer 2 (2023, Terminus as villain)
2024
X-Force: Necrosha (2015, Selene utilizes with the transmode virus to resurrect the dead Phalanx as an undead army under her psychic control that puts her in control of Genosha. It's the closest either Fox or Disney will ever get to making a Marvel Zombies film.)
Wolverine: Final Execution (2019, Sabretooth and Daken as villains. X-23 crosses over from X-Force. Daken dies. Nearly everything prior to Old Man Logan has happened.)
Fantastic Four: Frightful (2024, Doctor Doom assembles a team with the Mad Thinker, Trapster and Wizard to counter the Fantastic Four.)
2025
X-Men: Proteus (2023, Proteus as the villain, Moira MacTaggart who's the niece of the one we know from First Class is also somewhat villainous since she doesn't want to hide that she imprisoned her own son as a test subject)
Silver Surfer 3 (2025, Blastaar and Terrax as villains)
Deadpool 5 (2025, Evil Deadpool as the main villain)
2026
X-Force: The Dark Angel Saga (2026, Archangel becomes lured back by Apocalypse and may very well regain his place as a horseman executing Apocalypse's will. X-Force may very well have to murder their own close friend)
Wolverine: Not Dead Yet (2026, White Ghost as the villain)
Fantastic Four: This Land is Mine! (Lucia von Bardas as villain. The Fantastic Four are forced to assist Doctor Doom in regaining control of Latveria)
2027
Silver Surfer 4 (Obliterator as villain)
X-Men: The Twelve (2027, Apocalypse has returned. While X-Force may have delayed his plans, he may actually rule the world this time. Doctor Doom and Magneto are forced to assist both Cable and the X-Men in defeating this menace once and for all.)
Deadpool 6 (2027, Wackbeard the Pirate as the villain)
2028
Fantastic Four: Secret Invasion (2028, X-Factor discovers that Polaris was secretly a Skrull, worse yet, she was communicating with somebody in the Baxter Building. When one of the Fantastic Four is secretly launching an alien invasion, the team is pushed to their breaking point. Super Skrull is the villain)
Wolverine: Coyote Crossing (2028, Rojas as villain. Wolverine fights slavers in the Southwest)
X-Force: Zero Tolerance (2028, X-Force are on the wrong side of the law after the government reactivates the Sentinel Program which was led by a sentinel from the future who fled to the past during the time of DOFP. It's up to X-Force to stop Bastion and destroy any factory manufacturing sentinels. This is mutantkind's last hope)
At any point in the 2020s
X-Men/X-Force/Fantastic Four: Onslaught (2029, Onslaught/Dark Phoenix as the villain. One of the X-Men is a traitor and all eyes are on Gambit who was spying on the X-men for Mister Sinister until the events of Messiah Complex. Whichever one of them will become known as Onslaught is destined to not only slaughter the X-Men but most of the Earth's population. It turns out that it's Jean Grey who underneath Magneto's armor, is the Dark Phoenix. It's a way to take a mulligan on X-Men 3. By the end of the film, it's revealed that the Scarlet Witch created another pocket universe where she and Quicksilver were the only mutants in the world after witnessing the destruction caused by mutant powers. It turns out that without mutants, the world found others to become its heroes with Wanda and Peitro instead of being members of the Brotherhood being members of this world's version of the X-Men. X-Force and the Fantastic Four join forces and all three teams along with X-Factor from the TV series manage to stop Jean Grey but at the cost of their own world where they accept that their reality is dying after Jean destroys the M'Kraan Crystal watched over by Uatu which is causing the realities to merge. This results in the X-Men and Fantastic Four joining the MCU where the X-Men can team up with the Avengers, X-Force can meet the Defenders, X-Factor can cross over with SHIELD and the Fantastic Four can interact with the Guardians of the Galaxy and the Inhumans.)
