Bobby's little moment with Kitty—are his hormones craving physical intimacy that he's not able to have with his girlfriend? Or is he just doing something nice for a friend with no bad intentions or ulterior motives? It's worth noting that the kiss that was filmed but cutnote Filmmakers felt uncomfortable due to Bobby appearing much older than Kitty had Kitty as the one who initiated the kiss. So that puts her into interpretation - is she misreading Bobby's intentions (and she knows he has a girlfriend) or is she just caught up in the heat of the moment?
Rogue's attitude as well—does she have a legit reason to be suspicious? Or is she just paranoid and possessive?
There's also Jean not sensing Logan coming up to her during the final battle. Is she holding the Idiot Ball? Or is she holding back the Phoenix just enough to prevent her from killing him outright?
Contested Sequel: The film is either a bad representation of the Phoenix Saga and a total cop-out as far as the role of Cyclops goes, and being "The Wolverine and Jean Show" and devoid of all other character development... or it is an adequate adaptation of the Phoenix Saga that does away with plot elements that would have been out of place in the established movie canon, and a sweet action movie in which all hell breaks loose and Wolverine owns the show. A third camp feels that it's not as solid as the first two, but still nowhere near as bad as a lot of people say. Take your pick.
Critical Dissonance: The film had the worst reviews, but the best box office results out of the original X-Men trilogy, although a lot of that was banked on the goodwill from the first films, which were parlayed into a HUGE opening weekend for the third.
Beast, as played by Kelsey Grammer, was almost guaranteed to be this. His character managed to be a fan favourite despite the contested nature of the movie.
Kitty Pryde/Shadowcat too, due to getting an expanded role in this film. She had just achieved more mainstream popularity due to being featured in X-Men: Evolution. Also it helps that her actress Ellen Page went onto become a star.
Fanon: A common theory regarding the Continuity Snarl between X-Men: First Class and this movie is that the Xavier who visited Jean Grey was, in fact, a psychic projection. X-Men: Days of Future Past would later offer an alternate to this theory, with the presence of a serum that allows Xavier to walk, but takes away his powers if too much is used.
Fridge Horror: On the subject of the cure, it is very likely people will still be ostracized because they were mutants at some point. Imagine someone being seen to get it and get attacked later without being able to protect themselves.
The cure as a whole becomes horrifying when you consider the whole "mutants as metaphor" aspect of the films and comics—it can be compared to the concept of "curing" different minority groups, most obviously LGBT and disabled people. This can make it really horrifying for people in those groups when the cure is actively forced on some, and many others are pressured into taking it when they don't want to...
After watching X-Men: First Class (which revealed that the young Xavier taught Lehnsherr how to achieve greater control over his power by finding the point between rage and serenity—the latter requires a happy memory), Magneto's line of "Charles always wanted to build bridges" as he's moving a large section of the Golden Gate Bridge seems to indicate that he's thinking about his old friend instead of his mother in order to attain serenity. And like his mother, Xavier—whom he loved as a brother—is now dead, so happy memories from their brief friendship in 1962 is all Magneto has left of him.
Erik truly seemed to grow fond of Raven in X-Men: First Class and spent decades with her at his side, then casually kicked her to the curb in this movie after she was hit with the mutant cure. The disheartened look in his eyes for being forced to do so, however, cannot be ignored either.
Heartwarming in Hindsight: Professor X reassuring Beast that "You are always welcome here. You are a part of this place" becomes that much sweeter when you take into account their close relationship in X-Men: Days of Future Past. In between 1963 and 1973, Charles and Hank were each other's Only Friend after the former was forced to close his newly budding school due to the Vietnam War draft. Xavier then fell into a deep depression that was further worsened by his alcoholism, and McCoy did his best to try to take care of his former mentor. They eventually became Heterosexual Life-Partners, so Beast isn't just a good friend to the Professor; he's family. Hank also mentions to Logan that both he and Charles had built the school and the labs, so McCoy is just as essential as Xavier in the formation of the X-Men.
Beast throwing down the mutant cure in disgust is slightly amusing when you take into account his experience with another serum in First Class.
Kitty's and Bobby's relationship being a Not What It Looks Like situation for him and Rogue. Takes on a slightly new light now that Ellen Page is open about being a lesbian. Rogue really did have nothing to worry about. Bonus point for Anna Paquin admitting that she's bisexual, so is Rogue jealous on Bobby or on Kitty? (Additionally in New Mutants Vol.2, a lesbian member, Xi'an Coy Manh a.k.a. Karma, confessed her feelings to Kitty, who rejected the advance.)
Iceman (finally) came out as gay in the comics. Makes his semi-love triangle in the movie with two girls quite a bit funnier.
The Phoenix had meant to insult Wolverine when she tells him "What, you think [the Professor's] not in your head, too? Look at you, Logan. He's tamed you." In X-Men: Apocalypse, Jean successfully "tames" the Phoenix with Xavier's help.
The government hears that Magneto is raising an army to attack the mutant cure laboratory on Alcatraz. In response, they arm the guards there with mutant cure dart weapons in plastic dart rifles, the latter of which is sensible to stop Magneto but the former being Crippling Overspecialization at its finest. This only works because Magneto is equally stupid. They also leave Leech at Alcatraz instead of quietly moving him somewhere else when they know his life is in danger. Even though Magneto has a mutant sensor character in his ranks and would know they moved him, the government doesn't know that.
Magneto's plan involves uprooting the Golden Gate Bridge to bring his mutant army to Alcatraz. He could have just as easily dropped the bridge on Alcatraz, removing the need for an army entirely, or flown himself to an unreachable distance and turned the entire island and its large supply of metal (rebar, pipes, etc.) into a deathtrap.
Magneto just sends his army in with no plan, using them as fodder to determine the enemy's capabilities. As he demonstrates later, he could just have his A-list destroy everyone in a few moves and they would be powerless to stop him. This essentially serves no purpose but to make Magneto seem unsympathetic and callous to his own race. (A deleted scene does show Magneto try to get Phoenix to do something, which she refuses, telling him, "You're sounding like [Xavier] again." This does not excuse him failing to use his lesser, but still ridiculously powerful elites right off the bat.)
Magneto is surprised that the humans are using plastic guns. This from a guy who's not only been held in a plastic prison for quite some time, but has shown the ability to detect metallic signatures from far greater distances and act on them accordingly. He does so in this very film, in fact.
Magneto controls metal. Wolverine has metal bones and Colossus turns into metal. You would think Magneto would just toss them into the ocean (something he would do in a later film), but instead he leaves them on the battlefield.
The heroes need to stop Phoenix, so Wolverine is sent in to stab her with his claws. If he's in a position to get close enough to do that and you aren't going to make her vaporize his pants, then he should have grabbed some cure darts (which are literally everywhere) and cured her instead of killing her. Still psycho or not, she wouldn't be a threat. (Of course, you have to ponder if something like the Phoenix Force could be "cured" that way, but it was worth a try.)
Like You Would Really Do It: Magneto is stabbed with the cure. The movie's final scene shows Erik in a park, and a chess piece moves ever so slightly, implying the cure wasn't permanent. The events of The Last Stand seem to be Ret Gone courtesy of X-Men: Days of Future Past, though. Also, in that film, Future Magneto is definitely shown to have gained his powers back.
A lot of X-Men fans blame Brett Ratner for every single problem with the film. Others blame the film's original director, Matthew Vaughn, for screwing the film over by quitting right before the start of filming, and still others hold both men equally to blame. In actual fact, while you could make legitimate criticisms about both Ratner's direction and Vaughn's decision to quit, neither of them were responsible for the storyline. That was about 90% the same as the final film well before Vaughn had signed up, and neither director was permitted to make any serious changes to the screenplay (which, despite him giving "family reasons" for his decision to quit, was apparently a major factor in Vaughn leaving the film).
Ironically, many fans actually blame Bryan Singer for everything wrong with the film. Despite (or perhaps even because of) Singer departing the franchise to direct the similarly failed Superman Returns, and having nothing to do with the film at all!
Kid Omega's Intimidation Demonstration where he quills out in Magneto's general vicinity. Perhaps not silly itself, as it is clearly meant to evoke a scary animal's threat display, but utterly ridiculous when you learn that it's all his mutant power. That's correct, he is throwing his entire might on Magneto, which does nothing because it is literally next to nothing.
The whole exchange between Mystique and the guard in the prison truck.
Mystique:(posing as the President) Let me out of here! I demand that you release me! Do you know who I am? I am the President of the United States! Guard:Oh, Mr. President... Shut up! Mystique:(posing as a little girl) Why are you doing this? Let me out! I'll be a good girl! Please! Guard:(pulls out a can of mace) Keep it up...and I'll spray you in the face, bitch.
Magneto's line, "Charles always wanted to build bridges!"
Storm's passionate speech about how there's nothing wrong with being a mutant when Rogue asks if there's a cure, while well-intentioned, falls a bit flat when you remember that the woman who can control the weather is lecturing the woman who kills everything she touches about how she's wrong to consider getting rid of her ability to kill everything she touches and should embrace herself. The movie does point out that Storm is being a bit myopic and self-centred later, however.
One-Scene Wonder: The movie is full of them—Vinnie Jones as Juggernaut, Eric Dane as Multiple Man, Ben Foster as Angel.
Rule of Sean Connery: Ellen Page. Even a lot of the film's detractors enjoyed Kitty Pryde taking down the Juggernaut. These included Bryan Singer, who went on to bring Page back for Days of Future Past.
Scapegoat Creator: Brett Ratner picks up a lot of hate from fans of the X-Men for his role in directing this movie. Said fans tend to ignore the fact that Ratner joined the film's production at a relatively late stage (replacing Matthew Vaughn, who had been attached to direct for most of the film's development phase), thus minimizing the amount of creative input he could have possibly had to the movie.
Signature Scene: Wolverine killing Phoenix, Professor X's apparent death and the Juggernaut's "I'm the Juggernaut, bitch!" remark to Kitty Pride.
They Changed It, Now It Sucks: This film evoked this response more than the other films. Particularly killing off Cyclops anticlimactically and depowering Mystique—although this was partly a case of Real Life Writes the Plot, as the actors were unavailable for most of production.
The film in general is lousy with this, wasting not only the already under-utilized Colossus, but Psylocke and Multiple Man as well. Even Callisto could have gotten more characterization mileage than simply being another of Magneto's lackeys.
Cyclops, leader of the X-Men and arguably the REAL main character of the comics: the guy was less than a cameo in the movie. The character had to deal with the death of his lover, but apparently that wasn't worth exploring, nor were his actual leadership abilities. Also, with Xavier's death, the idea of Cyke taking leadership of the X-Men as a whole and not just the field team was very doable (he's been leader of the majority of the mutants for years in the comics), and would've made sense in the context of the story. But no, he was thrown out like yesterday's trash.
Basically, there are two kinds of characters in this film: on one hand, you have the characters who could all be the poster children for this trope. On the other hand, you have Wolverine.
They Wasted a Perfectly Good Plot: On the one hand, you have a member of the cast who turns evil, gains superpowers, and threatens to kill lots of people if she's not stopped. On the other hand, you have a "cure" for mutations, with some mutants wanting the cure while others afraid that it will be forced on them. Of course, since they are both in the same film, there is no time to explore either of them to their full potential. Not only that, the obvious justification for doing both in the same film, that the "cure" just so happens to be a solution to that whole Phoenix problem? It's never even considered.
Scott starts hearing Jean's voice in his head, calling his name. You'd Expect: That, being the leader of the team, he would (at the very least) go talk to someone about it, especially Xavier (who would be able to read his mind and figure out what's going on). Instead: He secretly packs a bag, blows off Logan (who tries to help him) and goes off to Alkali Lake by himself. There, he accidentally(?) awakens Jean/Phoenix, who then proceeds to de-atomize him. As if acknowledging Scott's actions, no one mentions him for the rest of the film. Stuffed into the Fridge and Sudden Sequel Death Syndrome, indeed.
Prior to the events of the film (and the trilogy), Xavier implanted a series of mental mindblocks in Jean's mind to prevent a latent personality (Dark Phoenix) from taking over. You'd Expect: That anytime over the last twenty-plus years, Xavier would have at least mentioned this information to Jean for her own safety. Not even when she's brought back to the school from Alkali Lake does he bother to come down and see her (when she's feeling conflicted about her identity) and try to restore the mindblocks. Instead, he's teaching a class. Instead: Jean, more pissed off than ever, takes up residence at her old home, and Xavier willingly walks in (with Magneto, no less) to try and reason with her. It ends about as well as you would expect.
Magneto wants to kill the mutant whose DNA is being used to create the anti-mutant serum, who is located on Alcatraz Island. Magneto, in a stupendous display of power, lifts the freaking Golden Gate Bridge to get to Alcatraz. You'd Think: that since Magneto wants to kill this particular mutant, and doesn't really care about civilian casualties incurred in the process, that while he was lifting an object hundreds of feet in the air that weighs over 1000 tons, he'd just drop it on their heads or turn it into a blizzard of shrapnel to tear every living being on the island into shreds. Instead: he uses it to form a bridge, marches across it and digs in for a long, difficult, and unsuccessful siege of the place.
The Woobie: Cyclops. Plenty wanted to give him a hug during the film. And then Jean killed him.