So, it's been pointed out, with the use of Quicksilver and Scarlet Witch in the "Ultron" movie, that the reason this was allowed is because they were both part of the Avengers team at some point, and Marvel has the rights to use any member of the team(paraphrasing my understanding of it). Also, it's been said that another studio owns the rights to the Hulk movies, but again, he's an Avenger, and thus able to be in those movies, but we won't get a Marvel Hulk movie. That being said, could Marvel simply use Spider-Man, Wolverine, and others in the Avengers movies?
Since they are crossover members, they could technically use characters that go by that name, but "with certain restrictions".
Consider Scarlet Witch and Quicksilver, who were originally introduced in the comics as Mutants, back in X-Men issue #4. They have specific backgrounds (e.g. they are the children of Magneto) and sources of their powers (born with them).
In the Fox-Movie universe, Quicksilver is a mutant, born with his powers, and there's even a quick nod in Days of Future Past to his possible parentage.
In the MCU, their parents are dead, and their father is presumably not Magneto, and their powers were given to them via experimentation. In fact, Scarlet Witch's powers aren't even her normal comic powers.
This all falls in line with the rumors that Marvel was allowed to use the characters as long as they made no mention of any "mutants", as all of those rights are held by Fox.
The same would go for any other characters left out of Marvel's ownership rights, unless they came to a specific agreement. Without permission from, or an agreement with Sony (thankfully, they worked one out!), Marvel would have to change Spider-Man dramatically - something they could probably get away with with characters like Quicksilver and Scarlet Witch, as they're lesser known by the average viewer, but not really the case with Spider-Man or Wolverine.