So, Marvel recently managed to get the rights to use Quicksilver and the Scarlet Witch in their Avengers movies, and also managed to get the rights to use Spider-man in their movies with a tighter relationship with Sony. I have some speculations on how they managed to do that.
The key is that Quicksilver and the Scarlet Witch have generally been better known in the comics as Avengers than as mutants. Sure, they have the relationship with Magneto and have been in the Brotherhood at various times, but most of their main storylines were as Avengers. I suspect that Marvel argued that while they don’t have the rights to X-Men characters, they have the rights to the Avengers, and thus characters that were in the Avengers are fair game in, at least, Avengers stories. Fox could have argued that, but since these two characters were well-known as Avengers and less so as X-Men, this was the case that, if they were going to lose it, they would, and losing the case might result in a broader interpretation than they liked. So they let it go, and made sure they put Quicksilver in the next X-Men movie to maintain their right to use those characters even if they were also in the Avengers.
Now, Spider-man has actually been an Avenger for quite some time now, and so I suspect that they went to Sony and made the same argument. Sony would have had a better case for claiming that Spider-man is better known as a solo hero than as an Avenger … but they also didn’t have any team affiliation for Spider-man either, which would lead to the argument that Marvel can use him in a team and they only have his solo rights. Since Spider-man isn’t an X-Man, that doesn’t leave Fox with an opening to argue that they can thus use him, too. Sony also isn’t knocking Spider-man out of the park and isn’t competing as much with Marvel over this stuff, and so likely decided that playing ball and getting the free promotion from Marvel was worth more than they’d get from fighting it, and so gave in.
The evidence for this is that recently Marvel has started adding more and more mutant characters to other teams, particularly the Avengers, and downplayed the X-Men. Kitty Pryde was also with the Guardians of the Galaxy for a while. Deadpool joined the Avengers. They had an entire mixed X-Men/Avengers team for a while. All of these seem aimed at one thing: associating X-Men characters with the Avengers so that Marvel can claim that they can use them in Avengers storylines.
Now, the most interesting character in this is actually Wolverine. He joined up with the Avengers at about the same time as Spider-man … before Marvel started having success with their own movies. Thus, an argument that they just added the character there to get around the Fox rights to the X-Men won’t really fly (like it would for the others). But Wolverine is clearly an X-Man first and foremost. It’ll be interesting to see if Marvel tries to get Wolverine into the Avengers movies, and if Fox will let them get away with that.
Anyway, just speculation. I have no inside knowledge and even lack a lot of outside knowledge here, but it seems to work for me.