These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
No superhero crossover film had ever been done beforenote At least for American superheroes, and most of Marvel's biggest supers were in the hands of other studios. All they had were mostly B-listers. Even the Nick Fury stinger at the end of Iron Man was inserted mostly then as a Mythology Gag. Great idea in hindsight, though, right? In fact, because of the MCU (especially The Avengers), said B-listers were elevated to near-Spider-Man status.
This has also affected every film since the Avengers. A third Iron Man and sequels to both Thor and Captain America? And yet critical response was mainly positive. Then they really took a gamble with Guardians of the Galaxy, with characters obscure even to Marvel fans, and again it turned out everyone loved it. And now Ant-Man will be a dud apparently, mostly due to Edgar Wright leaving.
Author's Saving Throw: After complaints about the female/minority superheroes not getting their own films Stan Lee revealed at a fan expo that Black Panther was getting his movie right after Ant Man and Dr. Strange, as well as that apparently every superhero will get a film eventually. This helped to placate quite a few fans.
Base Breaker: A frequent complaint of most of the movies is that the villains are boring- only Loki and the Winter Soldier have avoided this due to being both heavily attractive and being masterfully acted. Guardians got hit the most of this in Phase 2, thanks in part to being after two movies with Loki and Winter Soldier, and due to having to set up the five Guardians and being the start point for the Cosmic Marvel Universe, as Ronan and Korath both were called boring, with Nebula being the only real villain to have any sort of development.
A minor one but some feel that there's too much comedy in the films. It doesn't help that a big part of the appeal for the MCU amongst fans is that it's Lighter and Softer than many comics nowadays, so those who like the comedy get pretty defensive.
Some feminist and social justice advocating fans complain about how many heroes are a White Male Lead. This may be quieting down now that Black Panther's film has been confirmed.
Some feel that SHIELD has too big of a role and steals the spotlight from the heroes, while others like the concept and are happy that SHIELD is getting some focus.
Complicating this is how an MCU adaptation would have to be drastically different from the original, which had the US government starting up a Superhuman Registration Act. Most obviously, there's the lack of any secret identities among the MCU's heroes, and any secrets they did have are public knowledge anyway after Winter Soldier.
The news that Iron Man will be in the third Captain America film, together with Chris Evans saying he wants to move on to other work, has a lot of people understandably worried about the MCU's biggest Spotlight-Stealing Squad taking part in what may be Cap's final appearance.
Agents of S.H.I.E.L.D.: The Clairvoyant aka John Garrett is the Big Bad of the first season of the Spin-Off. Heading the Centipede Project as a powerful figure in HYDRA, the Clairvoyant has superpowered individuals abducted and experimented on, implants his soldiers with Explosive Leashes, which he utilizes should they fail him or outlive their usefulness, had Coulson tortured to reveal the secret of his revival, and frequently kidnaps and threatens the lives of the loved ones of his "employees" in order to ensure their complete loyalty. At one point he implanted a SHIELD Agent with an Explosive Leash and forced her to work for him, work that included massacring a subway train full of bank security personnel to get what they were guarding. Later he implanted an Explosive Leash in Mike Peterson as well, abducted his son, and turned Mike into the cyborg villain Deathlok against his will. Despite his cheery demeanor, the Clairvoyant has no loyalty or empathy for anyone, not even to his undyingly loyalright-hand man, Grant Ward, whom he nearly killed to further his own plans. Later, he would force Ward to attempt to murder his two friends, Fitz and Simmons, in order to prove he's not weak. Ultimately, the Clairvoyant's true interest was extending his own life, and once he'd achieved that he went on to plan world domination.
Guardians of the Galaxy: Ronan the Accuser is a genocidal Kree terrorist and renegade wholly devoted to the destruction of the planet of Xandar. Disgusted by his people signing a peace treaty, Ronan is introduced to the audience by confronting a captive member of Xandar's Nova Corps, crushing the helpless man's skull with his Universal Weapon, and then bathing in his blood. Beginning the film as a henchman of the Mad TitanThanos, Ronan seeks to gather an item for Thanos so that he will destroy Xandar for him. Under Thanos, Ronan has committed multiple murders, including the deaths of Drax the Destroyer's wife and daughter. He later pursues the film's motley band of heroes to the space prison The Kyln, and orders a full massacre of every prisoner to leave no witnesses. When he realizes the power of the Infinity Stone he has been sent to retrieve, Ronan double crosses Thanos and vows to kill him after he's finished with Xandar. Assaulting the planet, he even orders his own men to become suicide bombers by flying their ships into Xandar, injuring and killing numerous civilians. After mocking Drax about finally remembering murdering his family, he declares Xandar "guilty" by his psychotic philosophy and attempts to purge it of all life. Brutal, violent, relentless and unforgiving, Ronan stands as an example of rage, fanaticism, unchecked hatred and utter cruelty, and really stands out in such a relatively light-hearted movie.
Creator Worship: Kevin Feige gets a lot of this from fans, some of whom have even argued that he's doing a better job with these characters than the comic writers themselves are. Though he's recently been taking heat from the reveal that the Wasp is a Posthumous Character in Ant-Man.
Joss Whedon as well, but that's par the course for Whedon.
SHIELD Agent Phil Coulson, aka "SON OF COUL!" So far he's gotten two separate one-shot short films starring him as features on two of the movie DVDs, his own digital comic spotlight issue, and an Earth-616 counterpart. Even when he was killed in The Avengers, fan demand for him was so high that Coulson was brought back to life and given his own TV show.
Despite not even appearing yet, Mockingbird has gained a lot of hype after she was revealed to be joining the cast of Agents of SHIELD. CBR's SDCC announcement poll actually has her announcement as the highest rated announcement of the second day, even beating Sam Raimi's Evil Dead TV series announcement, The Walking Dead season 5 trailer reveal, and Guardians of the Galaxy sequel announcements.
Thanks to Guardians Of The Galaxy Rocket Raccoon and Groot. Also Howard the Duck.
Similar to Mockingbird, Black Panther is getting a lot of hype and cheers before his movie's release date has even been confirmed.
Tony's Arc Reactor being a reverse-engineered Tesseract. Possibly confirmed as of Captain America, due to Howard Stark, one of the original inventors of the Arc Reactor, being shown recovering the Tesseract at the end of the film.
Loki letting himself be defeated at the end of The Avengersso he could be taken to Asgard and steal the Infinity Gauntlet for Thanos. Could possibly happen given how Thor: The Dark World ends with Loki seemingly usurping the throne from Odin.
Coulson returning in Avengers 2 resurrected as the Vision. Coulson was brought back from the dead via Project T.A.H.I.T.I. following Avengers but before Agents of S.H.I.E.L.D, but the Vision has since been confirmed to be JARVIS.
With Clint's absence during the bulk of Phase 2, a popular theory from non-Clintasha shippers is that he spent the time with Mockingbird, either having solo adventures or just relaxing and recovering. A slightly less-serious one is that he had to take time off following the Loki mind control thing and the subsequent breakdown he likely had, just as Selvig did (complete with naked Hawkeye).
A lot of this from the DC side tends to cross into Scifi Ghetto and Hate Dumb too. A lot of people have expressed the view that the MCU is for stupid children while The Dark Knight Saga, Man of Steel, and Arrow are 'dark realism', and as such are better/for smarter people. While this ignores that the MCU can be rather dark at times and has plenty of content that isn't really that kid-friendly (the fact there's a sex scene in the first twenty minutes of the first film in the MCU seems to be ignored and forgotten), it also ignores that the DC films are also still rather popular with kids despite their perceived maturity, that DC have had a lot of films with a similar tone to Marvel's current films, or, you know, that there's a difference between tone and quality.
With Marvel movies not made by Marvel Studios, such as Sony's The Amazing Spider-Man Series and Fox's X-Men and Fantastic Four (2015) series. A lot of MCU fans wish these franchises would revert to Marvel, so such films made after Iron Man (not before), like The Amazing Spider-Man and X-Men: First Class are often dismissed as mere cash grabs made just to keep the rights from Marvel Studios. On the other hand, there are fans who believe that Marvel Studios simply doesn't care enough to buy the rights back (which is an option for them), since they make money off Sony and Fox's movies anyway and Marvel's in-house movies are performing spectacularly on their own.
A few fans seemed to favour Ashley Johnson's character (the blonde woman who appears several times during the Chitauri invasion) as a potential love interest for Captain America.
Some fans feel that Captain America had a lot more chemistry with Black Widow in Winter Soldier than he did with Sharon Carter (who shares one scene with him), and that it ultimately went to waste.
Hawkeye and Widow are pretty popular, but are as of yet not in a relationship as far as we can tell. Widow denies any feelings for him, and while the two are friends, they don't have any obvious romantic intentions.
Hilarious in Hindsight: The fan theory of "Hawkeye was absent for most of Phase 2 because he was having adventures with Mockingbird" is this thanks to Mockingbird being announced for Agents of SHIELD season 2.
Only The Creator Does It Right: Disney's films made under Marvel Studios almost always receive better reception from fans and critics alike over Marvel movies made by other studios after the beginning of the MCU. The sole exceptions seem to be the critically-acclaimed X-Men: First Class and X-Men: Days of Future Past (particularly the latter), both of which were made by Fox - though even these are cause for a Broken Base among viewers.
Possession Sue: Both Widow and Darcy get this a bit; Darcy is pretty much shipped with everyone because she works well as a stand-in for the shipper, while Widow, as the only girl on the team, tends to have her uniqueness stripped away and used as a placeholder for some female fans to get together with the other Avengers...but mostly with Hawkeye. Sad, considering how well Widow was written in the films. That said, it is possibly due to how well Widow was written that the phenomenon isn't as prevalent as it might be.
Rescued from the Scrappy Heap: His role in the MCU, combined with Matt Fraction's epic-length Invincible Iron Man run, rescued Iron Man from the horrendous Dork Age he had been in since Civil War. On a larger scale it lifted him from the B-list to being one of Marvel's flagship characters like Spider-Man or Captain America.
All the corners of the slash shipping tend to argue quite a bit. Tony/Bruce, Tony/Steve, Tony/Loki, Tony/Coulson, Tony/Rhodey, Steve/Bucky, Steve/Sam, Steve/Clint, Clint/Coulson, Clint/Loki, Thor/Loki, etc. Any two of these that aren't compatible with one-another tend to argue a LOT. Then there's the inclusion of their respective lady friends...
Since even before she was cast and brought in, Mockingbird has been in one with Natasha over Clint. As Clint's most prominent relationship in the comics, Clintasha shippers who've read up on the comics knew Bobbi would come in between Clintasha, and so have made a frequent point to argue over her, while Bobbi/Clint shippers from the comics have responded in kind. With Bucky being present, it leads to a three-way shipping war between Hawkingbird, Clintasha, and Bucktasha.
What The Hell, Costuming Department?: With the sole exception of his suit in the first film, Captain America's various costumes have drawn criticism from some areas of the internet, either for being too camp and colourful, or for the cowl looking odd (The Avengers), abandoning the traditional stars and stripes (Captain America: The Winter Soldier), or for just looking ugly (Age of Ultron). Obviously, many disagree though, but its a popular sentiment.
Hawkeye's suit in The Avengers also drew criticism for being his original Ultimate Marvel uniform, and got criticism for not being like his classic Marvel outfit. The creators listened and in the second film he's gotten an awesome new outfit that's a mishmash of his various costumes from the comics, complete with Badass Longcoat.
The Woobie: Captain America, Star Lord, Agent Coulson, and Winter Soldier.