Rogue
The Cure, for sure, is temporary. Humans will never get successful with it. Humans will remain humans, animals will remain animals, mutants will remain mutants. So Rogue and Mystique will regain their powers back.
Rogue will meet Gambit. gambit2 They will be romantically involved with each other. She'll kiss him only to discover her powers back... and absorbed every thing in Remy.
Cyclops
Scott did not die. It would be nonsense if he died. So how could he be alive? I am thinking that somebody might have had rescued him. Jean was kissing Scott yet Storm and Logan came only to see the unconscious Jean. So why was she unconscious? I was thinking there was a fight between her and "somebody". Couldn't this be Madelyne Prior? or Emma Frost? or the Hellfire Club? And this triggered Jean to become ferocious Phoenix.
The movie version for the Hellfire Club would consist of Mastermind, Maddie, Emma, and Shinobi. They keep Cyclops. They would want to get into X-Men for some reasons... probably Gambit (the Hellfire Club and the Thieves Guild for that matter, can be possible too).
Mystique
Mystique will regain her powers back and reform the Brotherhood knowing that Magneto apparently lost his powers. She'll be the team's newest leader.
Magneto
Magneto didn't lose his powers. He wasn't even injected with the Cure. Well, what can Magneto ever do with a metallic needle? And, hey... Magneto loves surprises. He always surprises the X-Men, he can do that to us - the fans.
Professor X
Professor X, while controlled by the Phoenix, exclaimed, "Jean, let me in!" That's it. Charles travelled into Jean Grey's mind. They met there. They wandered elsewhere. The Phoenix Force is controlling her body but Jean can nevertheless overcome her. She can redirect Charles' body away from the Phoenix at a blink of the eye.... so we haven't noticed it. How about the thing or the "body" that blew up? it wasn't Charles' body, it was just his clothes.
Jean Grey
Did Jean Grey die? Yes and No. Yes, her replica as used by the Phoenix Force died as killed by Logan. No, the original Jean Grey is still there inside a healing cocoon underneath the Bay ... alive.
So, see you all in X4.
gambit2