Actually, after doing all that, I came up with this. It's a synopsis of another movie I cam up with based on your ideas, stuff from the original film and and a few ideas I've thrown in there. Feel free to pick it apart as I've done to your ideas.
Cyclops, still reeling from the death of Jean Grey, is neglecting his duties as team leader, resulting in a training session almost going badly wrong if not for the intervention of Wolverine. Seeing Professor X, he agrees to take some time off and pull himself together. At the same time, a new student, Remy LeBeau, is admitted to school, takes the name Gambit and attracts the attention of Rogue, much to the disapproval of Iceman, while Colossus gets close to another new arrival, Kitty Pride, aka Shadowcat.
Meanwhile, Magneto and company have been hitting governmental institutions to try and validate their arguments over mutant superiority. In response to this, the government, in collaboration with Beast, have been coming up with ways to tackle the issue. They decide on the Sentinal program, a series of powered armour suits that the military has been designing. Beast is horrified by this, claiming that the government will use the Sentinals to repeat the concentration camps of WW2. He tries to convince the government to try less militaristic options, but is shot down and arrested, though he escapes.
Cyclops is drawn to where Jean died, where he finds her. She's not herself, and before he can talk to her, she vanishes. Reporting to Professor X, X uses Cerebro to tracks her down, and the pair go to find her, with Wolverine 'secretly' following (the Professor sensing him, but letting him follow them just in case). Finding Jean Grey, Cyclops tries to talk to her but she has a breakdown and turns into Phoenix. Wolverine enters and, realizing she's going to do something drastic, throws Cyclops out a window, leaving him and Professor X in the building. Jean then destroys the building, attempting to kill them both as Cyclops watches in horror. Wolverine recovers, revealing he shielded most of the damage, but the Professor is badly injured and in a coma (y'know,
again).
Cyclops, angry and confused about what has happened to Jean, returns to the school and tries to get the team to track her down, but when Beast appears and informs them about the Sentinal program, Wolverine admits that this is the greater threat and the team needs to focus on that rather than Jean. Furious, Cyclops resigns, leaving to find her. Gambit and Rogue have also gotten closer, which sets Iceman off as he tries to break the two up, leading to a fight. During this Gambit is injured, which causes Rogue to fling a metal girder at Iceman, hurting him as well. She doesn't know how she did it and is immediately resourceful and runs off, with Shadowcat running after her.
Magneto and his team encounter the Sentinals and a massive fight breaks out with bystanders getting caught in the fray before the mutants win. Mystique exclaims that she didn't sign up for people to get hurt - this was about mutants proving that they are who they are, but innocent people don't need to suffer to prove it. Before Magneto can respond, Phoenix appears and counters Mystique. Mutants like her are superior and humanity needs to accept this, whatever it takes. Magneto, recognising a new ally, immediately takes her in, leaving Mystique shunned.
The Sentinals then attack the school, but the X-Men, with the team fractured, struggle to fight them off until Mystique returns and uses her first-hand experience of them, along with help from Beast, to defeat them. Hearing about Prof. X's demise, she vows to help the school remember his dream of a world where mutants and humans could live together. Shadowcat returns with Rogue, and Mystique helps her to come to terms with the fact that she has Magneto's powers as well as her own. They bond, and Rogue apologizes to Iceman. Gambit, frustrated, walks off until Wolverine reminds him that there are more women out there then he can count - and he'll be able to actually touch them. Another friendship is formed.
Magneto and co, meanwhile, are taking the fight against the Sentinals to the government, and attack place after place. Even Magneto is shocked by how violent Phoenix is being, but she puts him in his place by reminding him that mutants are strong and they need to prove it. Cyclops shows up and challenges her, but Phoenix is having none of it and flings him around like a doll, almost killing him until Magneto secretly saves him at the last second and leaves him a clue as to where they'll be heading next.
Cyclops contacts the X-Men and once they find him, he tells them where Magneto and Phoenix will be - the primary manufacturing facility of the Sentinals. Although barely able to stand he insists on leading the team, and they head for the facility. The final battle is a three-way fight between the X-Men, the Sentinals and the Brotherhood, and it's an epic battle. Seriously Epic.The Sentinals quickly realize that they need to back out, but Phoenix is having none of it and wipes them out, humans and all, with barely even a second thought. Realizing that Phoenix want far more than he does, Magneto allows the X-Men to get close to her, resulting in Cyclops and Wolverine getting close to her. Seeing both men gets her to drop her guard and beg them to kill her lest she be consumed once more, but Scott can't do it. Wolverine, however, can and does.
In the aftermath, the government realizes that challenging the mutants is not a satisfactory option and seeks out more diplomatic solutions with Beast... and Mystique. The Brotherhood goes off on their own, with Magneto especially struggling to come to terms with how he should best accomplish his goals, while Cyclops accepts his place as leader, Rogue accepts her new abilities and relationship with Iceman, Colossus and Shadowcat accept their feelings for each other and the X-Men accept that they're stronger together than apart. Gambit even meets a cute mutant called Siryn
who can do amazing things with her mouth...
Post credits stinger: The Professor takes a breath... and flatlines. Is he awake? Is he not? Cliffhanger!