A thought came to me recently.Could it be possible that Scott is a skrull?
The way I see it is he would have been swapped out with the Skrull around the time him and Emma started dating. That was when he too major leaps in his morning by moving on to Emma, and also started to act like a different person and was suddenly full of doubts as if he wasn't used to being the leader of the X-Men. And before anyone says Emma Frost would have been able to tell with her telepathy even Charles Xavier couldn't tell if someone was a Skrull.
Now this is where the thought comes to mind. The X-Men didn't interact with the rest of the super heroes during the invasion. The role of the X-Men was very isolated, so it's very possible for a Skrull to slip by if they were in the X-Men. Next is how the Skrulls reacted to the X-Men. they were completely shocked by the presence of X-Men. Now I find it hard to believe that the X-Men would be over looked by the skrulls. It makes me think that their agent in the X-Men might of betrayed them, and given into the persona they were posing as, and that's not such a crazy thing because there was the one Skrull in the initiative that decided he liked living on earth as a hero better then fighting for the skurlls, the first Hank Pym Skrull was killed because he was starting to act too much like Hank Pym, and the Mar-Vell Skrull decided to be Mar-Vell and not the Skrull he really was. so I don't think it would be too crazy for a Skrull to take Scott's place and then found that the mind of Scott Summers was too much for him and fully embraced the role as Cyclops. Also all of Cyclops' close friends that have know him for years now hate him and can hardly believe that it was Scott that did all of this, as if it wasn't Scott at all. And I know Scott wasn't with the rest of the people they saved, but then again neither was Blackbolt because they wanted to use him as a weapon, and when Scott fully cuts loose his eye blast are likely stronger then any blast a Skrull cruiser could make.
In All New X-Men young Scott ran off on his own. Maybe he'll be the one to save real Scott? After all the whole reason the young x-men came back was to save Scott. Also They just had the traitor advertisement.