Gotta remember that if the X-Men and Spidey franchises are making money, Disney and Marvel are getting their cut of the profits. As long as those franchises are making money (ie, moviegoers are going to watch those movies) Disney/Marvel aren't going to bother re-purchasing those contracts. You gotta remember, if they do get those franchises back, they'll have to reboot and retool them if they are going to integrate them into the MCU. I'm afraid the X franchise would get a major retooling and probably make some diehard fans moan and groan.
The Fantastic Four...yeah, where's the reboot. Its been about 7 years since the Rise of the Silver Surfer movie came out. That's a long time it seems for Fox to sit on that contract without doing something with it other than getting a script writer.
Spider-Woman...I'm not sure if Sony has the rights to that character. Many may argue that she is not really related to Spider-Man, but to the average moviegoer I think there would be a huge amount of confusion if, by chance, Disney/Marvel came out with a movie that included her and find out that she has nothing to do with the Webhead.
Boy, I really liked the Secret Wars (the original). It had a simple premise that almost seemed to follow an old Star Trek episode's plot: a superpowerful being scoops up good guys and bad guys and tells them to fight. No long, lengthy explanation of who, how, what or where. There would be some problems with a movie version. If, by chance, Disney/Marvel had the movie rights to all their characters, how could they afford a movie that included HOW MANY big name actors, all the special effects, locations, etc.? The movie would be a major undertaking.
What about the villains? There were a lot of villains in Doom's group, a lot of which would need a lot of explaining if dropped into a movie.
I'm thinking that if they were to do a Secret Wars movie (or a Civil War movie, for that matter) they'd need a lot of groundwork done first. That groundwork would be more origins movies, more Avengers sequels, etc. That's going to take a lot time and that introduces another problem: unlike comicbook characters, actors age. How many more Iron Man movies is Robert Downey, Jr willing or able to make? Yeah, they can get someone to take over the role, but are they going to "act like RDJ acting like Tony Stark"?
I'm thinking if they were to make a REALLY GOOD stand alone ANIMATED movie, it could work. I'm not talking cell animation, I'm talking a major CGI movie (with performance capturing??). I haven't gotten into all of the animated movies that Marvel's put out. I'm sorry, but to me, they look juvenile. Yeah, I can get a good laugh and get entertained from some animated "kids" movies (Over the Hedge, Up, Wall-E, etc...and I'm sure a lot of people of all ages loved those movies as well) and even marvel at a good story shown in CGI animation (Disney's latest A Christmas Carol) but if this stand alone movie were to be really good, it should be geared for older audiences, not just a "cartoon that adults can enjoy." Why animation? I think it would help set itself apart from the MCU. If its in its own seperate continuity they can do a lot of explaining away for certain villains.
Also, and I just thought about this, I believe Disney/Marvel has the animation rights to ALL OF ITS CHARACTERS. That would really help free Disney/Marvel up to do a project like this. I'm not sure if Fox or Sony would complain that "Hey, this animated movie you're making is geared to be a major motion picture, not just a glorified Saturday Morning cartoon."