A couple of ways I think Marvel can use characters that are hard to do.
Ultron
Recently we have learned that Hank Pym will not be in the Avengers: Age of Ultron. If your a person who likes movies sticking to the comics (Like me) you will be... at least a little mad at this. My personal thought is just because Hank Pym isn't in the movie, doesn't mean he can't make Ultron. Have S.H.I.L.D. make Ultron. Then show the origins story after that. You don't need a lot of depth into the creation of Ultron, just how he turns evil and such. Have Hank be the "Lead scientist" In making ultron and leave it at that. Then if needed have Hank Pym in his movie talking about how he made Ultron. I know there are lots of other ways to make ultron like Stark, but in my opinion the failing of Ultron means as much as the failing of Harvey Dent in Batman. Keep him in the story please Joss.
Spider-man
Everyone should know Spider-man is owned by Sony. Now we all know about the attempt to put Oscorp Tower in the avengers. This is my idea on how to put him in the marvel universe (Without buying him form sony). Have Cameos/estereggs. Lots of them. Make it clear that this guy is in new york in the same universe that the avengers are. You don't need to have him in the avengers, true comic fans know he isn't a huge part of the team. A lot of his villains aren't much above street level villains. So let him deal with all of them while Thor, Cap, and iron man take down aliens and such. Besides those, I think the best possible cameo would be something along the lines of Nick Fury talking about trying to find spider-man but how he is to hidden to find. I don't know how this would work legally, but if they where going to put oscorp in the avengers, I think this works just fine.
X-men/Mutants
Probably the hardest to do. Mutants are owned by 20th Century Fox. Now X-men: Days of Future past is a story line that has time travel. We have heard from the director that it will fix issues in the Last stand movie. Now make this an alternate universe (Like what Star Trek did). Have it pretty much Reboot the series for another trilogy or what ever it is they want to do. Next would be how to make them work with the Marvel Cinematic Universe. Here's my idea, since Scarlet Witch and Quicksilver are in the avengers. Just make them piece keepers or something along those lines to separate the worlds. Let the Mutants fight their wars, and humans fight theirs. Think about it, the X-men movies have BARELY involved humans dying except last stand. Just keep their wars to themselves. Have cameos in avengers and X-men movies or eastereggs. At the most put wolverine in a Avengers movie (Marvel could pay 20th some cash for 1 movie). This way we have the X-men in the same universe as the avengers. Not quite full on coexisting, but they are about as close as they can get legally. Maybe a crossover movie is possible but that seems even harder at this point.
Fantastic Four
Buy them... I can't think of many ways besides that. You can do the same thing with the X-men, just let them fight their own. But they don't have the same ability to just ignore S.H.I.E.L.D. They are Humans, and I Don't see them being able to work alone very often. Its hard enough with the Hero's we have now to make them working alone seem legitimate. They could do it, it would just be a little forced past one movie. The reason I say they could do 1 movie is nobody would really know about them that much. They could fight Dr. Doom, but after that. There isn't much of a way to hide from S.H.I.E.L.D. for any more movies.
Daredevil
Again doesn't fight the world destroying villains, so just let him guard hell's kitchen. You can have S.H.I.E.L.D. talk to him, but let him turn them down. You can get at least 1 good movie, maybe force 2 with him and Electra. I think they could be successful movies that don't have much change in the entire marvel universe.
All in all just my opinions and ideas. I can't wait for all the marvel movies to come out. Also can't wait for the rest of the phase 3 movies to be made official. )