Marvels universe isn't one. I mean, it's not a universe. It's a multi-verse consisting of several universes that sometimes splash into one another. Among these several universes are the movie-verses of Marvel Studios, Fox and Sony. All separate, and occasionally referenced in comics like the Avengers prequel “Fury's Big Week”. With all the splashing of universes within the comics, it shouldn't be all that impossible for the movie-verses to splash a little into each other, which to some extent has already started happening with the reference to X-men in Amazing Spider-man 2s post credits-scene and the negotiations to put the Oscorp building into the Avengers (although the approval got in too late for it to actually appear).
Still, a lot of fans demand more. The inclusion of Spider-man in Avengers, a Civil War that includes characters from all three studios, Avengers vs. X-men and so on. I don't see this happening any time soon, because of the sheer amount of paper involved, both the printed kind with dotted lines and the green stuff would pile too high in a full-scale crossover scenario for it to be practical. Especially when the product can't be expected to be bigger than the sum of its parts sales wise (to dumb it down, the fans of X-men, Spider-man and Avengers overlap, which means a crossover-movie of all three, split three ways, will earn less for each studios than if they all just made another movie starring their characters. The same is true for a crossover between two studios). So a full on crossover is unlikely.
Where am I going with this? Well, while a full on crossover may be unlikely, we've already seen all three studios are willing to make at least a nod at each others movies, if nothing more. These are still three separate universes, though. And doing more than the occasional easter egg might upset the continuity. There would simply be too many questioning where Spider-man were when New York fell to the Chitauri, or why Iron Man or Captain America didn't intervene when sentinels started taking over the world. But if someone were to learn how to communicate between realities? Say, someone like Doctor Strange? I'm not saying this will, or is even likely to happen, but I can't see any good reasons the following scenario couldn't be coming somewhere down the line:
Sony wants to do a Spider-man movie focusing on the spider-side of Spider-man. Not just the powers, but the mythos behind it and the legends concerning spiders. Basically, they want to throw in Ezekiel, Morlun and Shathra from J. Michael Straczynski and John Romita jr.s run on Amazing Spider-man from the early to mid 2000s. Always interested in a little cross-promotion, they ask Marvel Studios if they're interested in lending away Doctor Strange for a cameo. For a tidy little sum, and the prospects of good PR for their upcoming Doctor Strange sequel (yes, this is likely to be pretty far into the future if it's at all possible), and only after reading the preliminary script for the scene, Marvel Studios agrees to give him one scene. Sony agrees and gets to work, first introducing Ezekiel as a guy with similar powers to Spider-man, who befriends him and starts asking questions about his origins. The crossover cameo scene is likely to be a dream sequence, where Doctor Strange warns Peter that he's been noticed, and found “interesting” to the mythical powers that be (you do not ever want to be “interesting” in the eyes of mythical powers that be. It never ends well for the people involved). The rest is Peter just trying to survive, as Morlun chases him around the city hellbent on “eating” his totemic nature, while Shathra decides to destroy Spider-mans civilian identity, ensuring only the spider remains when she starts hunting him.
This is, of course, wishful thinking on my part. But I do believe the first true crossover-scene between any of these three studios will be trans-dimensional in nature.