For no particular reason, I find myself thinking about all of the classic X-Men stories that Fox could have adapted for the movies, instead of falling into pretty much the same template over and over again, and wringing all of the life out of the series. And if you like them, I'm not going to say my taste is better than yours, just that even with Singer back, there are so many missed opportunities.
Before I dive into the storylines and character development that they could have utilized for the movies, I'm going to throw this out there--I'm not even going to mention the stuff that Fox doesn't seem to want to touch. No storylines with the Shi'ar, or Dire Wraiths, the Brood, or Mojo. Fox is focused on mutants as social commentary for oppressed minorities, and there is still plenty of classic X-Men storyline goodness they could have tapped, but didn't, or haven't yet.
Scott Isn't (Always) A Dick/Scott is a Good Leader
In the comics, Scott is the perfect student, and the perfect soldier. He does everything that Professor X wants him to do. But along the way, he actually becomes a good leader. Tactically, he may not be n Captain America's level, but he's not that far off. We also miss out on another storyline (later on the list) that would highlight this aspect of Scott's character growth.
The movies also had a chance to rectify the "Scott is a dick to the women in his life" trend that developed. Originally, Chris Claremont's idea was for Scott to get married, have a kid, and pass the torch of leading the team to Storm (more on that later), only to show up again in big summer crossovers when the X-Men needed to call in the reserves.
Alas, not only did the concept of X-Factor (the original series) trump Jean's sacrifice in the Phoenix Saga, it also laid the groundwork for Scott being a huge jerk to the women in his life. That said, keeping Scott from getting married and settling down frees him up for a relationship with Emma Frost later on (more on Emma later on the list), which actually produced some solid storytelling as well.
Wolverine is a Murdering Berserker
Wolverine, in the movies, moves around from where he was at in the mid-nineties, character wise, to where he was at in the 2000s. By that I mean, he went from a guy haunted by his past and all the killing he had done, to a grizzled veteran with an affinity for the younger X-Men, even as he tried not to be a role model to them. He was already the wise old ronin.
This skips the entire 80s feel of the character, when he was intentionally sarcastic and unlikeable, because he didn't want anyone getting close to him. He was honestly worried that when he got into a fight, he'd go into a berserker rage, and not be able to tell friend from foe, and being a jerk was the best way to distance himself from others.
Eventually, between Jean and Yuriko, he decided he couldn't keep distancing himself from others, and started to force himself to have more control over himself, and the berserker rage thing got to be less and less prevalent, except in situations of extreme stress. Even then, circumstances where he would have been the wounded, unthinking animal, he wasn't, because that's when he first got close to Jubilee (more on Jubilee later on the list).
Professor X isn't Always Going to Be Around
Several times in the X-Men's history, Charles disappeared. This created tension for the characters, and it also allowed Scott to step up and become the leader in his absence. It doesn't have to be permanent, but even for a movie or two, we would get to see how dedicated the students are to the teacher's dream, and how they interpreted it as they try to carry on without him. Sometimes the best way to show the long shadow that a character casts is to take him out of the scene.
Storm is a Good Leader
I was kind of shocked when I read an article a few years ago, talking about how perplexed someone was that Storm would get her own series, because she was just kind of "there" in the X-Men. I grew up reading stories of Storm stepping up, taking over the team, and being a kick ass leader that could whip people into shape in some of the X-Men's darkest hours.
I'll lump this in here, even though it could be a separate plot point, but part of what showed her leadership ability was that she still managed to be an effective leader even when she lost her powers. We started to see her picking up skills like piloting from Scott and self-defense from Logan, and how she became a lot more than her formidable powers.
Forge and the Power Neutralizer
First off, Forge was a great character to introduce just to explain all of your super science gadgets, since his power is to invent stuff that is way beyond modern science. Second, back in the day it was a big deal when the government hired him to create weapons that neutralized mutant powers. It wasn't permanent (although we weren't sure of that for a while), but there was a lot of angst introduced to the series once mutant hunting government types could just shut off powers during a fight (without going into the whole mutant cure thing from X3).
Beast, Iceman, and Angel Leave to Be Legit Superheroes
Obviously the Avengers can't be referenced by Fox, and probably not the Champions either. But I think there is some value to showing some of the X-Men leaving the team as the younger team members move up the ranks, to do some super heroics of their own. It even allows you to have a "rise and fall" arc where they are loved for being superheroes for a while, until something (probably beyond their abilities to thwart) goes wrong, and everybody hates them again.
This doesn't need to be it's own movie, but could serve as an interesting sub-plot that shows the world isn't just focused on what's going on at the school all of the time.
Emma Frost Has a Competing School
So much room to tell stories with this one. If Emma hadn't shown up back in the sixties, and not even remotely been Emma. Another school of mutants, one that wasn't being taught to make the world better so much as to figure out how to best gain power and influence using their powers, would have been a great contrast.
And while this would have been a separate plot thread, having Emma appear as the amoral headmistress of her own school would have made transitioning her to being on the side of the angels later in the movies more interesting. Don't make her super evil, but do make her arrogant and self-interested.
The Brotherhood Transitions
Oh, how off the rails has Mystique gone. Mystique's Brotherhood looked a lot different than Magneto's, and not because she had a few different members. Mystique was an opportunist more than she was ever a zealot, and we missed out on a great opportunity to see her sell out her team to Val Cooper to have them work as government agents hunting mutants for a while, to show how "not Magneto" Mystique really was.
How did Fox never use Genosha as a storyline? Not only does it play perfectly with their key central focus for X-Men movies, but it also lets you get away from real world governments and Weapon X always being the face of human oppression, which means you can really step up the oppression without feeling quite as heavy handed.
Genosha is a country that becomes the most advanced nation in the world because they make laws that say a mutants powers "belong" to the state, effectively making them into slaves. Then they tell the outside world that mutants are happy productive citizens that want to help make Genosha a paradise. This plot writes itself, and in multiple parts (see later in the list).
Magneto Takes Over Genosha
You really have to let Geonosha show up in one movie and just get to be evil, and yet have other nations refuse to get involved when they are actively oppressive mutants, and let that stand, and then let Magneto's assault on Geonosha be a separate movie.
What kind of thought provoking discussion do you think you can generate when a bad guy with good motives does horrible things to horrible people? How many real world parallels can you draw between a terrorist that becomes a head of state, and the fact that the world has to recalibrate how they view him and interact with him, once there is a totally mutant controlled state?
This would have been a much more satisfying development for Magneto than "he's friends with Charles, he's a good guy, he turns bad, he's friends with Charles . . . " repeated over and over again.
Master Mold as a Rogue AI
Master Mold doesn't need to be a giant Sentinel, just an AI that controls Sentinels, and comes up with the idea that humans and mutants aren't really separate species, so the only way to protect humanity from mutants is to run the whole planet, control breeding among humans, and "manage" the root problem with mutants, that being humans themselves.
On it's face, it's a standard "rogue AI" storyline, but it is also a way of delivering the message that humans really shouldn't be seeing mutants as anything other than an extension of themselves. And it gives you an excuse to have a Sentinal-centric storyline. If you really wanted to do it, you could also fold the destruction of Magneto's version of Genosha into this storyline, after you give Magneto his shining moment of giving mutants their one safe haven in the world.
Jubilee as Wolverine's Sidekick
Yeah, we kind of got Rogue doing this, but not outside of a full X-Men movie. I'm talking about a "solo" Wolverine movie where the school gets blown up, the X-Men scattered to the four winds, and Jubilee is the only person that has Wolverine's back.
It was never about how awesome her powers are(n't), but the fact that she is more than willing to risk herself to be there for Logan, and how having her with him humanizes Wolverine. Contrasting his new role as protector and mentor with the killers he used to work with coming back to haunt him in the present would be a great way to show some transition of how his character sees himself and his role in the X-Men.
Rogue Really Can Have a Good Storyline
It wouldn't be all that hard to introduce a mutant that was similar enough to Carol Danvers to allow Rogue to put someone into a coma, and be literally haunted by another personality trapped in her head, even as she had permanent access to a wider powerset. Coming to terms with what she did was a major factor in her development, as was her actually being raised by Mystique, which we also completely lost out on with the movie's weird alternate Mystique development.
Love is in the Air for Wolverine and Storm
It's fine to have Wolverine pine after Jean for a bit. And for a solo movie, you really need to introduce Yuriko into the mix for a while. But honestly, at least show some chemistry between Wolverine and Storm. If nothing else, it could make for an interesting storyline to have them get together and realize they are better friends than lovers.
Where the Heck are the Morlocks?
The concept that there are mutants with really extreme mutations that cannot live with normal humans and started to live in abandoned tunnels under New York is great. For maximum effect, you really need to introduce them in one movie, with them appearing to be a threat, and then becoming sympathetic, and then have a later movie depict the brutal attack of the Marauders on them, which gives the X-Men a serious knock down drag out fight against an evil opposite team.
How has this not made it into a movie yet? High tech zealots with body armor and weapons that have decided God Hates Mutants? I mean . . . how has Fox not used this yet? Sure, they already snagged their leader for a member of Weapon X, but that doesn't mean the group, as a bad guy faction, suddenly melts away.
All of that was pretty much just off the top of my head. I'm sure there are a ton of stories that don't have anything to do with aliens or magic and still focus on mutants and human rights allegories, that would be way better than constantly rehashing the same story elements over and over again.