Cash Cow Franchise: Two of the films have made over a billion dollars in ticket sales alone. Most franchises are lucky to get one movie that makes that much.
Colbert Bump: One of the benefits of not having Spider-Man and the X-Men available to use is that Marvel put their B- and C-list heroes in the spotlight instead, causing the likes of the Hulk and Captain America to regain the main stream notoriety they once had, saving Iron Man from slipping into C-List obscurity, and giving the Guardians of the Galaxy the main stream appeal they had never had before. The Guardians in particular went from struggling to keep a single comic on the shelves to having six solo or team books by the following year, their own cartoon, and more merchandise sales than they'd ever seen before.
Creator Backlash: Actor Terrence Howard was not happy at being dropped from the franchise due to being screwed over by Marvel. His contract stated he would paid $8 million for Iron Man 2, but the studio told him they would only pay him a fraction of that, and he could either take it or leave. He left and James Rhodes has been played by Don Cheadle ever since. He also claims that the most of the money in his contract went to Robert Downey Jr.'s salary.
Exiled from Continuity: Due to rights, the Spider-Man, Fantastic Four, Namor and X-Men characters cannot appear in Marvel Cinematic Universe as of now. So, while we can't see the Hulk fight Juggernaut anytime soon, there are gray areas. Some characters who are known to these groups, such as Cable, Dazzler, Quicksilver, Scarlet Witch and The Kingpin, are still usable, but they cannot mention their connection to those groups... which would be interesting to see, given Cable's tenuous relationship with the Summers line and Quicksilver and the Scarlet Witch being the children of Magneto.
And Phase Two is going to run into this head-on with Quicksilver (if you'll pardon the pun), as different versions of him are going to be in both X-Men: Days of Future Past and Avengers: Age of Ultron within a year of each other.
Per interviews given about Agents Of SHIELD, it's now confirmed that the MCU cannot use the word "Mutant", so they often use other nomenclature, such as "Gifted", for the mutant-like beings that show up on that show. Whether this is because of some sort of written agreement or just an over-abundance of caution about possible legal issues (as mutants and mutation are actual scientific concepts and are more-or-less generic terms) with FOX is unknown. Director James Gunn has confirmed that a similar joint rights agreement exists for the Skrulls, who are a general Marvel Universe threat but nonetheless debuted in the Fantastic Four. The alien race known as the Badoon are owned by Fox and off-limits to Marvel, which led to them being barred from appearing in the Guardians of the Galaxy movie (but not from making a cameo in one of the prelude comics).
Sony struck a deal to have Oscorp Tower from The Amazing Spider-Man appear in The Avengers, but the special effects crew was too far along to insert the building into the NYC skyline. Rumored discussions of a deal forming between Sony and Disney serve as a sign that Spider-Man will be the first major property to be integrated after another company rebooted the film franchise.
Namor is an odd case in that Universal (who currently owns the film rights to the character, although they have not used him) is supposedly interested in sharing the property with Disney provided that they can profit off of it. Man-Thing is in a similar position, where he is owned by Lionsgate, but the company isn't interested in making another solo film with the character unless they can reap a portion of the rewards. This got more complicated when Man-Thing was mentioned in an episode of Agents Of SHIELD, and given that no statement has been made regarding the character, it's completely ambiguous as to who owns the property.
A self-imposed example can be found in the form of Ant-Man; though Marvel owned the film rights to the character, Edgar Wright didn't want the company to do anything with him until he made a movie starring the character. After the Development Hell passed, the characters in that series are free to show up in the MCU proper.
Hey, It's That Guy!: A twofer — For all of the well known actors appearing in the films, and for the various cameo appearances in the films by characters from other entries in the universe.
Paul Bettany has stated that he sees his role as JARVIS as simply a source of easy money and has never even seen the Iron Man films. However, he's been much more invested in his new role as The Vision.
Bettany: "I used to be in a studio for 45 minutes and do J.A.R.V.I.S. and get a huge bag of cash and go my way like a burglar, and now they want me to work for my money. Which is great and sweaty and hot, which you’ll realize once they unveil everything. It’s really f***ing cool. It’s great to join this train which is on really clear tracks."
Glenn Close has said the same thing about playing Nova Prime.
Despite signing a multi-film contract, Hugo Weaving claims to have little interest in reprising his role as the Red Skull, having grown tired of blockbuster work.
Mark Ruffalo is this to Edward Norton as Bruce Banner in the Avengers movie.
Don Cheadle replaced Terrence Howard as James Rhodes.
Howard Stark has been played by a different actor his first three film appearances (Iron Man, Iron Man 2, and Captain America: The First Avenger). Somewhat justified on that last one, as Howard Stark was supposed to be about 20 years younger than he was in the Iron Man movies.
Zachary Levi replaced Joshua Dallas as Fandral thanks to his commitments to Once Upon a Time which is a reversal of The Other Marty, as Zachary Levi was originally cast as Fandral in Thor but couldn't because of Chuck related scheduling conflicts.
Josh Brolin portrays Thanos from Guardians of the Galaxy onwards, after Damon Poitier made a brief cameo at the end of The Avengers.
The Pete Best: Most fans generally forget (or prefer not to acknowledge) that Edward Norton was ever the Hulk. Technically this also applies to Eric Bana, who played him in 2003's Hulk.
Anthony Mackie says he wanted to play the Falcon to show the kids in his family (as well as black kids in general) that black people can be superheroes too. In general, he's been very vocal about the need for greater diversity in superhero movies.
Michael Douglas says this was his major motivation for playing Henry Pym in Ant-Man. He even took his son to Comic-Con to promote the movie!
Trolling Creator: It's been tradition since the first Iron Man to have a post-credits scene. Leading up to The Avengers, these scenes foreshadowed events that would be touched on in other films. Starting with The Avengers and continuing on in Iron Man 3, Thor 2 and Guardians of the Galaxy, these foreshadowing scenes are played mid-credits, and audiences who are Genre Savvy enough to wait to the end of the credits are rewarded with a pointless, humorous Brick Joke for their patience.
Despite huge demand, Kevin Feige (head of Marvel Studios) repeatedly said that there were no plans for either a Black Panther or Captain Marvel movie... right up until the Phase 3 announcements, where not only were both movies given release dates, but it was revealed that both had been in the planning stage for a long time and Black Panther had even already been cast and would be showing up in Captain America: Civil War.
A Runaways movie got as far as casting calls before they realized that it's just too complicated a mythology to dump into the franchise all at once (in the comics the plot ropes in time-travellers, mad scientists, aliens, crimelords, witches, mutants and pan-dimensional god-monsters, and that's just the origin), particularly before they'd even got the Avengers fully established. Of course now that they're brave enough to make something as obscure and bonkers as Guardians of the Galaxy it's safe to put it back on the "coming soon, maybe" pile.
The Wasp was initially going to be part of the team in The Avengers, and was even included in earlier drafts of the script. Joss Whedon is on record saying that he really enjoyed writing her, but ultimately had to cut her out of the script due to there being too many characters.
It now seems like Janet will not be in film - according to Michael Douglas, Janet dies while making the first Ant Man.
And now, Edgar Wright's Ant-Man, which could well have been one of the most individualistic visions within the MCU.
Early drafts of Guardians of the Galaxy had Nova as a central character. He was cut because they felt his character arc was too similar to that of Star-Lord, and because James Gunn does not like the character.