We have been through the alternate universe of x-men.   Someone goes insane, someone dies or whatever and bang a new and different reality.  

So if you could re-write the reality of the x-men universe what would you do, and if necessary, how would you cause it to happen?    

For me things started to go bad for the X-Men with the Mutant Massacre, and I think it was because Storm made a series of bad choices. 
 
1. She kept Magneto out of the tunnels, even after the Marauders wiped the deck with the team. There was only one Marauder Magneto was vulnerable to: Vertigo, everyone else he could have taken out by himself. Had Storm sent him in there he could have stopped the massacre and gotten a prisoner for Psylocke to interrogate. 
 
2. She did not call any other super team. She decided it was a mutant affair and did not let the Avengers or the FF know what was going on under their feet. Again, more manpower to stop what was happening and stop the Marauders from escaping, more manpower to track back to the real culprit: Mr Sinister. More connection with the real of the superhero community rather than isolating the X-Men further. And with the Avengers on board, they would have had legal clout to back up any prosecution.
 
3. She made an alliance with the Hellfire club, which did the X-Men no favors at all. She later left Magneto to interface with them, which destroyed the fragile trust he had built with the New Mutants and drew him into more nebulous activities. 
 
4. She faked the X-Men death, which again helped no one, furthered their isolation, made Magneto think that the entire fate of mutant kind had fallen on his shoulder as the Mutant Registration Act was passed, a mutant massacre had just occurred, and then Doug Ramsey was killed making Magneto's fall back to militantism almost inevitable. This decision also led to Outback years (as cool as they were) which then led to the splintering of the team as they were shoved through the Siege perilous. 
 
I would change all four of those decisions: I think that would have put the X-Men on a completely different path, especially in keeping them more in touch with the capes and tights community I don't think they would be as isolated and beset as they are now. In fact, as divided as the Marvel Community is, I think more solidarity and communication earlier on could have altered the entire course of 616 history since 1990.