I'm just reposting this from a different thread.
I hope that the plot is a mix of The Twelve, Endgame, Fall of the Mutants and X-Cutioner's Song. Sugar Man and Nemesis can be the two references to the AOA storyline, as can some level of time travel to bring young Charles Xavier and Gambit into the present.
The plot would be that Xavier gets attacked by a young Magneto who infects him with a techno-organic virus which kills him. Then Magneto/Apocalypse transforms into Onslaught who fights the X-Men to a standstill. Cable then intervenes and scares off Onslaught. Cable informs the X-Men that Xavier and Magneto were defeated by Apocalypse and they were both part of a prophecy foretelling Apocalypse's death. His plan to defeat Apocalypse involves traveling back in time, bringing Xavier to the present and then curing Magneto as he's become a horseman. He promises not to destroy time itself as a mysterious benefactor whom even Cable himself doesn't know, gave him the power to clone Xavier back in the 70s who would both age quickly and retain all of Xavier's memories. As Cable travels back in time, onslaught appears along with three others who Apocalypse merged with in different timelines, one of which is Angel who was cured of his mutation by his father and wanted to be able to fly again, the other two are a hideous creation known as Sugar Man and mysterious being named Nemesis.
Cable meets up with old Xavier, performs the process of splitting Xavier into two people and prepares to return to the present along with Magneto's daughter Polaris. Quicksilver doesn't trust Cable and demands that he come along, as Polaris is his sister while Havok and Gambit follow suit by demanding to go to the future to see Xavier. This is where Cable tells Havok that he's his grandson and all the proof that he'll need lies in our present day. Cable takes the four of them into the present, regroups with the X-Men, Wolverine kills Nemesis who Apocalypse claims was his son and then sees who Cable brought with him from the past. Young Xavier expels Onslaught from Magneto, turning him back into merely a de-aged version of himself. Apocalypse then summons yet forcefully converts Wolverine and Gambit into horsemen as vengeance while infecting a young Cable with the same techno organic virus which forces Beast to freeze him so he may be thawed out when the time is right.
Cable requires the Fantastic Four to meet him in Egypt where twelve heroes will defeat Apocalypse once and for all. Magneto and Polaris representing opposite poles, Storm, Human Torch and Iceman representing the elements, Cyclops, Phoenix and Cable representing the passage of time, Xavier being the mind, The Invisible Woman and Havok being space and time, and then The Thing as the core. Shadowcat, Colossus, Quicksilver, Rogue and Nightcrawler will handle the horsemen while Beast and Reed Richards ensure that Cable's younger self is able to be preserved for future generations.
Rogue is the one to defeat Gambit by stealing his power and reverting him back to his normal self while Colossus fights Wolverine, Quicksilver fights Sugar Man and Archangel does battle with Shadowcat and Nightcrawler. Apocalypse then informs the Twelve that even should they win, there are enough different versions of Apocalypse from different timelines that he WILL rise again. Apocalypse then engages in a massive battle taking place at the same time as the other X-Men fight the Horsemen. Cyclops deals the finishing blow to Apoclypse right as Apoclypse is about to kill Cable but with his dying breath he begins fusing with Cyclops before Cable defeats him for good by harnessing the same dark Phoenix powers that Jean used in X3. The world is saved, at least for now. Archangel joins the X-Men as with this timeline's Apocalypse now dead he's completely free of his control. Cable declines the opportunity to join saying that he'd rather travel the world now that his horrible future never existed.
Mid-Credits scene. Gambit, Havok, Quicksilver and Polaris are walking down a street in San Francisco when they encounter Rictor and Multiple Man. They explain that they are part of a temporal anomaly and worth studying. Quicksilver replies that he's not a lab rat. Another Multiple Man appears and then tells him that he's with the military and is far more interested in recruiting them, then a third Multiple Man asks Havok as ex-military himself, if he'd like to lead.
Post-credits scene. Cable's "mysterious benefactor" is cloaked in shadow but visible enough to be seen drinking some sort of liquor in a rather expensive looking chair. He picks up the phone and asks if Nathan Summers figured out who he was, he then says, "No? Then all is going according to plan. Shaw's killer should now be lucid enough to truly pay for his sins. (pauses and nods) Yes, Mister Creed, he travels with Lensherr now as well, You will have your vengeance as well." The mystery man then hangs up his cell phone, turns off his antique phonograph and we see Sinister's face emerge as he leans forward and cracks a smile.
See people, AOA isn't needed as a storyline to tell this and still be true to the comics.