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.
Alternative Character Interpretation: When the Phoenix 5 were flying all over the world creating their "Pax Utopia" were they really trying to improve the world because improving the world is the ultimate goal of any hero, or were they just wanking off at themselves and their new power and taking advantage of the chance to take all their oppressors and effectively imprison them?
Did "Pax Utopia" ever stand a chance of truly being paradise or was it just a prison where the Phoenix 5 could subtly abuse every and anyone who had ever wronged them (remember, in the name of "peace" and supposedly encouraging humanity to "go and build great things" the Phoenix 5 destroyed all the worlds weapons, or as many as they could get their hands on, thus making it impossible for humanity to attack them)? After all, nice weather, plentiful food and maybe even health care aside, a prison by any other name is still a prison no matter how you dress it up.
Does being mind controlled by the Phoenix truly excuse Cyclops, Emma, Namor, Colossus and Magik for the questionable and in some cases just straight up horrible things they did?
Ascended Meme: Cyclops predicts the rise of the "Cyclops was right" meme in-verse.
Ass Pull: The "Anti-Telpathy" nano-machines Tony Stark creates and injects into all of the Avengers specifically so Emma Frost can't end the event in issue 2.
Dan Slott (who has a flair for these) supplies a humorous one in the final issue of Vs. for a couple of the more ridiculous victories in prior issues. Turns out Squirrel Girl and Pixie, completely ignorant of the conflict, were playing an RPG with the Puppet Master's voodoo dolls. It's somewhat unclear whether this was intended to be canon, but more than a few fans accept it.
Broken Base: This event should have been titled "Avengers Fans vs. X-Men Fans".
Either you think the Avengers were assholes who came to San Francisco in bad faith ready to kidnap a kid for dubious reasons with no intentions of negotiating or you think that they were justified because the Phoenix is a giant threat, has been a threat in the past and they have to do anything necessary to stop it from potentially destroying everything.
Either you think that the portrayal of the Phoenix as a destructive entity is fine and in line with the most well-known Phoenix story (The Dark Phoenix Saga) or you feel like it's a flimsy premise that ignores 15-20 years of Rachel Summers' existence and her bonding with and complete control of the Phoenix Force (although this is YMMV, as Rachel largely controlled the Phoenix by never trying to access its full power, and even she did slip sometimes).
Either you think that the actions of the Phoenix Five are in line with the corrupting influence of Phoenix Force or that things are being wildly exaggerated for dramatic effect with the main group being written incredibly out of character.
Either you take it as given that the Phoenix Five made the world a utopia, or you take it as a given that they did so by quashing free will across the planet.
Either you think this story is the natural climax/ending of Cyclops' character arc since Messiah Complex or you feel that his Jerkass qualities have been taken over-the-top to justify the actions of the Avengers. If not, you either consider Cyclops a villain who's finally getting what he deserves, or you think he's basically a victim to the Avengers who's been pushed to the very end.
Either you think that Captain America was right in presume over Scott's mental condition, and his lack of open remorse is evident of his fall from grace, or you think he's a detached political sock puppet incapable of recognizing how Scott had been carrying on his shoulders a situation for years so impossible that if one, and only one of his friends dies in an attempt to stave off genocide, (of the usually hate induced variety), rather than say, a bus full of children, then it was in fact a very good day,and think Cap's reaction to his imprisonment are, at best, embarrassing. Just as embarrassing is the fact that Cyclops, in Smug Snake mode, was clearly goading Captain America into taking a swing at him.
Everything in the story and even the very existence of the story itself really is grounds for heated arguments. Which is probably the point, really, as the Avengers and X-Men have wildly different ideologies and themes that are often debated even when the characters themselves aren't punching each other.
The Avengers and anyone siding with them. To X-Men fans, they've spent the entire story acting like giant antagonistic jackasses and are essentially responsible for most of the bad things that happen (mainly by showing up, telling Cyclops they're taking the potential savior of his near extinct race and that's that; and again when Iron Man's "brilliant plan" causes the Phoenix Force to be split and create the Phoenix Five). Issue 11 pretty much pushes it over the top despite the fact the Avengers are, nominally, the heroes of the story. Acknowledged in the last issue, where Captain America realizes that the Avengers have been pretty crappy heroes when it comes to mutant affairs.
Wolverine specifically fell under this early on in the story, as his solution to dealing with the Phoenix was to outright kill the teenage girl who was the intended host before the Phoenix arrived, which went much farther than the Avengers merely wanting to take Hope off-world in the event that she was unable to control the Phoenix. However, he soon backed down from this line of thinking when he realised he couldn't go through with killing a child. In Consequences, Scott really lets Logan have it over this.
Designated Villain: Cyclops' X-Men, and later the Phoenix Five. At least, until they become corrupted by the Phoenix Force and start acting more like actual villains. Even then, Cyclops could still be a designated villain, as he only gets consumed by the Dark Phoenix after much poking and prodding by the Avengers and the X-Men. Until that point he kinda kept his sanity, at least compared to his teammates.
Magnificent Bastard: Cyclops is an Anti-Heroic example, particularly in Consequences where he displays that he knows how to play him some serious politics.
Emma has two possible moments thus far. In the Avengers Academy tie-in, she scraps Juston Seyfert's pet Sentinel, simply for being a Sentinel, while in issue 9 of the main series, she telepathically kills a man who had killed a mutant child thirty years ago in a hit and run, and kept it a secret.
The Avengers invade the sovereign nation of Utopia, take (almost) the entire mutant species prisoner and hold them in concentration camps where their powers are disabled
Namor's assault on Wakanda, which likely killed countless civilians.
The prison where Scott is being held in Consequences crosses when they allow Scott's new friend, a newly-activated mutant, to be lynched by the other inmates. This causes Scott to accept Magneto's offer to break him out.
One-Scene Wonder: Rachel's delivering a Curb-Stomp Battle against both Captain America and Thor received the greatest praise from both her fans and detractors of this event.
Signature Scene: The choking scene in issue #11 was framed as being the most brutal moment of the event up to that point with a mostly silent double-paged spread and images of Emma screaming horrifically and then laying still with blood coming out of her mouth.
Some Anvils Need to Be Dropped: Cyclops and Captain America moralizing to each other is undoubtedly divisive but both deliver a message that the other needed to hear. Cap calls out Scott out on risking the entire planet with his assumptions and that whatever good he has managed to do does not outweigh all the damage he helped caused. Scott similarly points out that the X-Men have been standing on their own in the world with the Avengers never getting involved beforehand and that they can't just go swooping in and expect people to follow when they have no reason to.
Strawman Has a Point: Both the Avengers and the X-Men make some quite frankly idiotic decisions but their motivations for those decisions is hard to fault at points.
On the Avengers side they want to take Hope somewhere where she can't do any damage in case she can't control it. The way they try to do this could have been handled better but there were very real concerns behind that decision. Wanting to the minimize the damage from a cosmic powered entity is honestly just good sense, especially considering the Phoenix unrestrained can destroy star systems. As Cap points in his What the Hell, Hero? speech to Cyclops he was assuming that the Phoenix was there to restore Mutants as a species, essentially risking the entire planet to restore a minority of the people that lived there. There is also the fact that despite the X-Men having greater experience with the Phoenix the entity is incredibly temperamental on a good day. Not to mention that the Avengers were proven right when Hope couldn't even bond with the Phoenix properly.
On the X-Men side they want to keep Hope on Utopia based on the idea that the Phoenix will allow her to restore mutants as a species. While this is risky based on how unpredictable the Phoenix tends to be it should be noted that the X-Men have a much greater understanding of the Phoenix than most people, especially since one of their members was a host for it and never lost control. Cyclops thought process also shows a rational understanding of the nature of the Phoenix Force in that he understands the loss of an entire species would attract the attention of such a life giving force. Their complaints towards the Avengers about staying out mutant affairs carries some truth with it as well.
Scott Summers: All I wanted to do was change the world. To see my children grow up to be something other than time-traveling freedom fighters. To see mutants able to use their powers for more than just fighting killer robots."
They Wasted a Perfectly Good Plot: Interested in seeing what this utopia the Phoenix Five created is like? Too bad! The reader is merely told that they P5 made the world a perfect place. Actually seeing any of that, examining the morality of a benign dictatorship, seeing what the ordinary person thinks about the benevolent cosmic-powered mutants who took over the world, etc., would get in the way of more punching.