Awesome, Dear Boy: Glenn Close was ecstatic to play Nova Prime in Guardians of the Galaxy, having always wanted to play an M-like authority figure. By all accounts she enjoyed filming the movie and immediately said she was eager to return for a second.
Cash Cow Franchise: Three 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. As of Avengers: Age of Ultron, it has taken Harry Potter's spot as the highest grossing film franchise of all time.
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.
Joss Whedon has expressed some regret that Marvel's insistence that he helm Age of Ultron prevented him from working on Agents of S.H.I.E.L.D.
Actor Terrence Howard was not happy at being dropped from the franchise due to being screwed over by Marvel. His contract stated he would be 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 most of the money in his contract went to Robert Downey Jr.'s salary.
Jeremy Renner wasn't happy with his Brainwashed and CrazyAvengers role that kept him out of the team dynamic for most of the first film, saying it "wasn't what I signed on for"; Whedon placated him with a much beefed up central role in Age of Ultron.
Darkhorse Casting: To an extent. For the most part Marvel Studios prefers to cast more obscure actors or have them Playing Against Type as the film leads, while relegating more famous actors to side characters. As a result the films tend to be a Star-Making Role for them.
Dawson Casting: In a weird way. The new actor for Spider-Man in the Marvel Cinematic Universe is 19 year old Tom Holland, who people claim "looks too young" to play 15-year old Peter Parker. Given that Tobey MacGuire and Andrew Garfield were both in their late 20s when they first started their own movie franchises - a Peter who was a late teen, at best - this is particularly absurd logic.
While not an extreme case, Hayley Atwell is older than Peggy Carter in the 40s-based scenes - she was 28 when filming a Peggy who aged from her early-to-mid 20s, and plays a late-20s version when Atwell herself is in her early-30s. In the same context, Dominic Cooper plays Howard Stark aged in his mid-to-late 20s when Cooper himself was in his early-to-mid 30s age range
Development Hell: Before ever getting its own studio, Marvel had plans to produce films of Iron Man, Thor, Ant Man, Black Panther, Iron Fist, and Luke Cage. Now, this is a reality (although Iron Fist and Luke Cage will be television properties).
Executive Meddling: Ike Perlmutter and a select group of cronies kept interfering with Kevin Feige and the film properties. The stress this caused played a large part in people like Jon Favreau and Joss Whedon declining to return to the franchise. After Disney purchased Marvel, Feige invoked a higher level of meddling, threatening to walk unless Perlmutter was cut off from Marvel Studios entirely. Disney obliged by restructuring Marvel so that Marvel Studios became a separate entity and Feige didn't have to answer to Perlmutter anymore. This caused so much relief that Chris Evans even said that he might consider extending his Marvel contract (he'd previously been adamant that he'd leave once it was over, due to Perlmutter).
Due to rights issues, the Spider-Man (until February 2015), Fantastic Four, Namor and X-Men characters could not appear in Marvel Cinematic Universe at the time it was created. 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.
Phase Two ran into this head-on with Quicksilver (if you'll pardon the pun), as different versions of him were in both X-Men: Days of Future Past and Avengers: Age of Ultron within a year of each other. The Avengers version died, which would leave things wide open for the X-Men version... except moves have been made in the comics to cut his and Scarlet Witch's ties to the X-Men franchise.
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).
The Hulk is also in a form of exile, as while Marvel has development rights to make movies with the Hulk, Universal retains distribution rights to get them into theaters. Hulk characters can show up in ensemble movies no problem, but there's no incentive for Marvel to make a Hulk standalone movie if they have to split the profits with someone else.
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."
Clark Gregg says this was initially the case. He took the role of Agent Coulson only as a favour to Jon Favreau, his neighbor at the time. However he ended up enjoying the role more than he expected, leading to Coulson becoming a Breakout Character.
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.
Edwin Jarvis (Howard Stark's butler in Agent Carter) and JARVIS (Tony Stark's AI in the Iron Man movies) are technically variations on the same person, in that the latter's voice and personality are based on the former. However, they're played by different actors (James D'Arcy in the TV show, Paul Bettany in the films).
James D'Arcy normally plays slimy villains, and he plays the bumbling and pompous Edwin Jarvis. He was reluctant to take the role for this reason.
Playing Gertrude: Some actors across the franchise portray characters older than they are, notably:
John Slatterly portrays the older Howard Stark from content set in the 70's and after, starting with Iron Man 2. Slatterly was about 47 when he began playing Howard, who was officially 53 when his son Tony was born in 1970.
Hayley Atwell portrays Peggy Carter in every time period the character appears starting with the early-40s and ending (so far) with 2014, averting Time-Shifted Actor; Peggy is born in 1919, and Atwell herself was in her late-20s when she first assumed the role. See also Dawson Casting above.
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. The trolling has become almost poetic in its inconsistency, as inter-spliced with the Shmuck Bait stingers above are the legitimate post-credit scenes of Winter Soldier and Ant Man, and the complete absence of anything at all at the end of Age of Ultron.
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.
Before this became reality in February 2015, Sony was keeping their options open to cash in on a Spider-Man crossover, but their new reboot has proved enough of a success that they've decided not to cut the pie. It wasn't until the negative reception the 2nd movie received and the damaging hack of Sony did Sony change their minds about doing Spidey and MCU crossovers.
And speaking of Spidey, the Oscorp building was originally going to be in The Avengers, but the film was too far in post production to include into the movie.
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.
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.
Regarding the sequel, Gunn's original script was to introduce two new characters as future team members. He decided however that one of them would need to be cut, stating that despite their being a "fan favourite", he had enough returning characters (and their own storylines) to juggle and feeling that the plot would become over-complicated if he kept them. That said, he hasn't ruled out bringing them into a future instalment, should he return to direct yet another MCU film.
Inhumans was originally going to be released before Infinity War Part II, but the unexpected addition of Spider-Man pushed it back to a few months afterward.
Similar deal with about half of Phase Three. If you believe Kevin Feige, this wasn't entirely unplanned - in his words, they were considering the possibility of Spider-Man joining the MCU since October 2014, when the Phase Three slate of films was first announced. The initial announcement was "Plan A", which would involve no SM, because though they weren't sure how the chips would fall; "Plan B" was to push all the films after Guardians 2 to later release dates (save the Infinity War duology) if their bid to get the Spider-Man rights succeeded, but they didn't want to announce it in case the Sony negotiations completely broke down.
Things were adjusted again when Ant-Man proved successful enough for a sequel - it got the July 2018 release date of Black Panther (which was moved to February 2018), and Captain Marvel got a second push-back to March 2019 (presumably to prevent four movies needing a release in 2018).
Before getting the part of Falcon, Anthony Mackie said that he wanted to play Black Panther; nonetheless, he has shown zero regret about getting the part and is supportive of Chadwick Boseman being cast in the role.
Djimon Honsou was another actor who hoped to get the part, and even still held out for the possibility after his role as Korath in Guardians.