Me personally, I would start with the Second Genesis. Open with a flashback of the O5 as teenagers, and skip ahead a few years. Center the first movie around Prof. X/Cyclops' recruitment of Storm, Nightcrawler, Colossus, and Wolverine. Cyke trains them (right down to giving Wolverine the hands just to show him who's boss), and they are sent on a mission to rescue the OG X-men from Stephen Lang (rabid anti-mutant ex-govt scientist) and his sentinels. The final battle consists of a knock-down, drag-out brawl with both teams mowing down waves of Sentinels. Escaping from Lang's outer space research facility, Jean sacrifices herself by flying the shuttle (like in the comics) so that everyone else can escape, and resurrects as the Phoenix at the end. End the movie on a bittersweet note that Jean will be OK.
For the next one, introduce Lilandra. Start with Prof X's nightmares and premonitions of destruction, and introduce Lilandra as a stranded Shi'ar empress. Magneto has returned with his Brotherhood, and they stole her technology to fuel a doomsday device to destroy all humans (like in X1). Without that technology, Lilandra can't repair the M'krann Crystal either, meaning the destruction of both her empire and Earth. The X-men from the previous movie all return (Cyclops, Storm, Wolverine, Nightcralwer, Colossus, and a recovered Jean) alongside with a couple of new recruits like Rogue (and maybe Gambit).The climax consists of a final showdown in the depths of Magneto's volcano base, where the X-men don't do so well against the villains until Jean's Phoenix powers re-awaken. With her Phoenix powers, she overwhelms Magneto and saves the day. His machine destroyed, Magneto swears vengeance and escapes to strike another day. Lilandra is able to recover her technology, and both worlds are saved. However, a mysterious figure known only as "Jason Wyngarde" is trailing the heroes, watching Jean's abilities with great interest....
Finally, Fate of the Phoenix starts in medias res, with the X-men showing up at Warren's New Mexico, badly battered and bruised after several run-ins with the Hellfire Club inbetween movies. They regroup and decide to investigate the Club itself, like in the comics. Jean is mindcontrolled by Mastermind and turned against the team. They manage to beat the Hellfire Club, but the damage is done-- Jean goes bad! She curbstomps the team, flies out into space, rampaging and destroying planets. The X-men calm her down in a rematch (with the help of Prof. X), but Lilandra returns and is out for blood. The final act of the movie climaxes with the X-men's showdown with Lilandra's Shi'ar imperial guard on the moon. The X-men fight valiantly, but are overwhelmed, and Jean ends up making the ultimate sacrifice for the good of the universe. Kitty Pryde shows up to the Mansion for the first time after the funeral in the very end...