What's clear is that she was their leader. We don't know what plans they have for the future, but as of this movie, she acted as their leader. Everyone looked up to her, she took charge, she gave a speech, and at the end they were all standing before her. Also, focus was put on Cyclops just as much as it was put on Jean. Nothing indicated that he was leader or that he was going to become leader. He just had a big part. Big deal...
I don't want this to be an argument, let's refrain from words like "You're also putting way too much stock into this." As that can be taken a little mean...ish? To someone who analyzes stories and even a writer
So of course I over analyze things. It's kind of my thing *wink wink*
Anyhow back to the debate on hand
I don't see how Mystique was hinted to be their leader. Yes, they all looked up to her because of the events in Days to Future Past. This much is very clear. What I saw was Mystique training them, it was shown a little more boot camp style imho. Part of the reason I believe that is because they are all fresh and as green as they can get. Training them in the Danger Room shows her more of a teacher than a leader. They look up to her and that makes her the perfect person to teach them to become X-Men. I felt that Cyclops's story was leading up to him taking over a leadership position, quite naturally to be precise. No pun intended xD When he spoke people naturally responded, gravitated to him. To me it was his character development that shows all roads leading to this. As for Mystique. She never really was an "X-Men" in the movie. She walked that middle ground, she distance herself from the X-Men because of her beliefs. She's admired because of them, but it also shows that she has a darkside as well. Something that these new "Greenies" haven't seen yet. Her relationship with Professor X is very close and he sees her as a sister, so he forgives her for her mistakes. There are many people that look up to Magneto, and Mystique is one of those people.
You're also putting way too much stock into this. Just because they're using characters and plot points closely related to Cyclops in the comics, doesn't mean he's suddenly the central character in all this. These movies don't even acknowledge that Mystique is Nightcrawler's mom among tons of other things because of how badly they've butchered everything. What makes any of this any different? For all we know, Mister Sinister is a one time villain for Wolverine 3, the next X-Men movie is all about the phoenix, and Cable isn't even related to Cyclops or their relationship just isn't important and is never elaborated on.
It's quite clear that it's different from the comics. There isn't really much to argue otherwise
I feel like we need to assume that Mystique will not be Nightcrawler's mom in the movies for a number of reasons. One of them being age. It would be very weird and if it does occur. It'll likely be a mistake on the writers part. Or Mystique is older than we previously thought (unlikely) or has a much darker past than we were lead to believe.
As for Cable and Cyclops not being related. This is a very good point. It can go either way, we don't know. Given that time travel is a huge plot point in the films. It could very still he is son. Depending on how they connect that or how it's portrayed. It may very well just be dropped as an Easter egg. There is no hints or anything to suggest either or, but there is an opening there and they could reveal that he is his son at any time. Even if it's years down the road.
While we don't know anything about Wolverine other than Hugh Jackman claims it's his "Last movie". Something he said before, and that Patrick Stewart will return as Professor X. It's also rumored to be the "Old Man Logan's" story arch, as I am sure you are well versed on this rumor
It's also rumored that Liev Schreiber will be returning as Sabertooth. I think this is very likely and Liev himself has suggested this. There is also a likely rumor that the movie will be "R" rated. I think this might occur and Hugh Jackman wanted "The Wolverine" to be rated R.
Hugh Jackmans set pictures certinatly line up wit the "Old Man Logan" rumors.
http://www.lazygamer.net/entertainment/first-wolverine-3-set-pics-show-old-hugh-jackman/
I don't think that Mr Sinister will be having a large role in this movie other than something more or less Weapon X related. It's very likely that Laura Kinney, aka X-23 will be making an appearance in some form, as I suggested before. It seems like an obvious route and she has potential. I just hope they give her a lot of depth to her character than just being some clone of Logan.
Then there comes the ultimate rumor. The one that has been demanded by many fans (most requested villain I believe) is debatably Wolverine's greatest rival and adversary. The perfect send off for a Wolverine film. The would be none other than Omega Red. The rumor is that Boyd Holbrook may be playing Arkady Rossovich. With the rumors of the villains being "Cybernetic". His cybernetic implants certainly fit the bill. Last but not least. Omega Red can drain the life force out of his victims. What would be a better way to have Logan himself look aged and drained. Given the way Wolverine is presented in the films. I cannot think of a better way for Logan to become Old Man Logan other than getting the life drained out of him. I know the original X-Men isn't cannon now, and I can't recall at the moment, but didn't Rouge drain him when they kissed? I think Omega Red would be the most interesting and most intensive villain they could use. A true send off for the fans and Hugh Jackman himself.
