Here are a couple of pointers that will be addressed in the next sequel:
Case 1: Rogue
We saw Rogue go to the clinic to get the cure because her powers weren't allowing her to get in physical contact with her boyfriend, or anybody else for that matter.
We didn't see her get in.
She didn't explicitly say that she took the cure.
For all we know, she probably learned to control herself.
Xavier: if she held on any longer, she could have…
It appears Rogue is the only one with the power to Kill Logan who is otherwise indestructible. If anyone were to finish off the X-men, they’d have to kill
If Magneto still has his powers, Rogue probably still has hers as well. Now assuming that Magneto is pissed at the X-men (Logan in particular) for taking away his powers, he would obviously make them his enemies and want to kill them. This is where Rogue would come in.
Charles made it clear that Storm, not Cyclops would take his place when the time came (a clear indication in the movie that Charles was soon to die and also that Scott would have a similar fate).
We'll get to see Storm as the new leader.
This is just speculation, but I see a relationship between Storm and Beast.
He has no idea how the indestructible metal alloy which restricts aging and gives him healing powers got into his body structure.
Magneto: You haven't told him (logan) about his past, have you?
Xavier: His mind is still fragile
I believe that X4 could finally answer those questions. From X2 with Striker, it was clear there was something that happened to him that only Magneto, Striker and Charles knew about. When Charles was talking to
Case 4: Magneto
This is what will spark the next installment. Magneto just slightly moved the iron pawns when playing chess--a clear indication that his powers weren't completely suppressed. That little bit of hope could bring back the old magneto.
Now if this is possible with magneto, why not with Mystique and Rogue?
-And by the way, Cerebro still exists. With Jean and Xavier dead, who’ll be able to control it?
-Stryker is presumably killed in the X2 explosion. If he resurfaces, which i'm almost certain he will, he'll try and attack Kitty Pride