Here's a very simple proposal as example of connectively through various franchises.
X-Men - Establish Havok and Cyclops with some family issues along with a traditional team like Beast, Gene, Storm, Rogue, Gambit, and Angel. Interject Cable as an antagonistic ally who respects Cyclops. Then have Sinister kidnap Scott & Jean to use them with the remaining X-Men saving them.
Wolverine: Enemy of the State - Wolverine tracks down a Yakuza plot to America to perform an assassination, but is subdued by the Silver Samurai and brainwashed to attack several members of the X-Men including Jean who were in the way of the plot. He recovers and stops the plan, engaging in an uneasy truce with the team.
Deadpool: Suicide Kings - Deadpool is framed for a murder he didn't commit after learning of his wife he thought was dead. To complicating things the man who framed him goes by the name of T-Ray, and claims that he is actually Wade Wilson, sending Deadpool on a question for his own identity, eventually leading to a teamup with Cable.
StarJammers - Following up on Havok's and Cyclops' family troubles, Havok leads a team that includes Jean Grey to track down his youngest brother Vulcan who has left to confront the Shi'Ar, our first contact with intelligent life who he believes to be his true ancestry. During the initial attempts by Havok to convince Vulcan to return and the Shi'Ar's first offensive, Jean is killed in a solar flare. There he challenges Gladiator for rule of the empire, and is stopped only when Jean returns as the Phoenix.
X-Men: XSE - In Bishops dystopian future, a man named Stryfe has dominated the land, and he comes across a clue from Jean Grey that claims someone betrayed the X-Men. He consults his old friend who was alive to witness the downfall of the X-Men, but is then forced to contend with a prison outbreak from one of Stryfe's men known as Fitzroy, who Bishop follows into the past to defeat beside the team he always idolized.
Cable: X-Cutioner's Song - Cable, still at odds with the X-Men still shows interest in contacting Scott. He has his own team of mercenaries known as X-Force, including Domino, Warpath, Wolfsbane, and Deadpool, when the villain Styfe appears having been lead back during Bishops journey to the past. During the final confrontation he learns that Stryfe appears to be Cable himself.
Gambit: Honor Among Thieves - Rogue journeys to find Gambit in New Orleans, where a war between an Assassin's and Thieves guild is ignited by a plot to bring the dead back to life, including Gambit's ex-wife. Meanwhile Bishop is acclimating himself to the X-Mansion where he discovers that Gambit shares a striking resemblance to his friend the Witness. Recalling Jean's warning, he races to confront him, as Rogue learns more about Gambit's seedy past than she wanted.
X-Men: Fatal Attractions - A plot against mutants inadvertently frees Magneto who tries to return the favor devastating the entire Earth from his new base Asteroid M. In the process of stopping him the X-Men storm the base and in his rage he rips the adamantium off of Wolverine's skeleton. Scarlett Witch, Sabertooh, and Mystique are all defeated.
The Death of Wolverine - In a feral rage, Logan ventures into the wild with only his bone claws, hunted by Sabertooth who seeks revenge for the defeat of Magneto at the hands of the X-Men. In the process he is hunted by other forces like Omega Red, and observed by a mysterious presence. In the end, victorious, he is found nearly broken and restored as the Horseman Death by Apocalypse.
Excaliber: Legion - Professor X's son goes insane with voices in his head encouraging him to murder. He is hunted down by a team of Nightcrawler, Psylocke, Shadowcat, and Colossus. They encounter Cable, who's ship Legion steals, forcing him to reveal it's capability to time travel. Following him, they save a young professor X and bring Legion back to the present where he breaks free, and is ultimately able to kill his father, as we find elsewhere Apocalypse was the guiding voice and stands with his horseman beside him.
X-Men: Age Of Apocalypse - A distraught Cyclops is confronted by Bishop who reveals that in his time Jean had spoken of a traitor, and suddenly a devastating attack is laid on a major city by Apocalypse, Sinister, and a very young man named Nate, who he says he named after himself. Cable offers his services to Cyclops who accepts, while Apocalypse corrupts the Scarlett Witch as his last horseman to accompany Wolverine, Abyss, and Holocaust. Excaliber, X-Force, and the X-Men join together, while the StarJammers are in pursuit returning to Earth with the Phoenix. Logan and Wanda are subsequently cured, but the later is left distraught.
Cable & Deadpool: When I Was Your Age - Cyclops and Gene Mary, and the story follows Cable's path away from the wedding where he meets Deadpool and over the course of nearly a year, the two share stories of their past, including the death of Wade's parents, along with Cable's future, and the revelation that Stryfe might have been his future self. It is Deadpool who pieces together that Stryfe must have been the creation of Sinister by fusing Scott and Jean, and that Cable must be their son. All of this while the spend months tracking down the leader of a cult known as the One World Church. They return just in time to see Cable born.
Wolverine: Daken - The Phoenix has restored Logan's humanity, and after Apocalypse regrafted his adamantium, he was given parts of his past memories as well, including the existence of his son Daken. In pursuit of him, he encounters many obstacles including Lady Deathstrike, and feels as though somebody is controlling him. In the end he frees Daken from the burdensome hand of Romulus.
X-Men: The Phoenix Saga - The Shi'Ar return to Earth, seeking justice for the disaster caused by both Vulcan and the Phoenix. Cable arrives with a desperate confession to Scott and Jean, that he is their son, returned from the future. He says they must send their young son Nate to a safe place in his future before the impending war takes place. What he doesn't tell them is that subsequently Scott is killed, sending Jean into a rage in a fully powered Phoenix form, in which she decimates the Shi'Ar, and becomes a danger to Earth, unable to regain her personality. In desperation, Scarlett Witch, after Magneto's actions, the terror of Apocalypse, and the unlimited destruction of the Phoenix, utters the phrase, "no more mutants", and a confused human Jean falls to the ground.
Magneto: House Of M - With only a few mutants retaining their power, Magneto has few challengers to his reign, and he immediately dominates human society.
Cable: Messiah Complex - A new mutant is suddenly born, and to prevent Magneto or other from claiming it, Cable escapes to the future with her. However, Bishop now fears that this is the harbinger of the horrible future he grew up in, and chases Cable through time to kill her, creating the destruction he was raised to fear. Hope, as she is called, ages, and in the end, returns to the time they left, Cable now as an old man, and Hope standing before the remaining X-Men as the last hope against Magneto.
What?!
