Arc Fatigue: With the announcement of issue #9, many readers started to feel this burn, mostly due to the fact that it seemed to just take so long and they wanted it over.
Doctor Doom is the godlike ruler of Battleworld. Fans are split between if it's cool and makes sense, considering the character's status in Marvel history or they are annoyed that it's basically handling all the glory and honors to him and in the tie-ins everyone has to bend their knee to him.
Sheriff Strange. You either think it makes sense or you are annoyed that a cool character like Doctor Strange has been reduced to basically Doom's First Asskisser. In Issue 3 it is revealed that Strange is indeed aware of what Earth was like before the event, and is simply acting as Doom's lackey to fill the role, which may make this better or worse depending on the viewpoint.
Broken Base: The Reveal of Doom's face under his mask. While some praise the looks of the face, some also have rallied because it was expected, after all of these years, to be worse (and some even think that it shouldn't have been as scarred — Doom being Doom, he probably would have exaggerated how bad it was as another reason to hate Richards).
Catharsis Factor: Sure, Doom is no saint either and uses their power to rule Battleworld as a tyrannical deity, but to see him outsmart and kill the Beyonders, who were destroying all of the multiverse purely out of boredom, is nothing short of satisfying.
Even people familiar with Marvel might have trouble understanding everything about this series and its many tie-ins without doing some research beforehand. This was inevitable, considering how the event pulls so much of multiple Marvel continuities into it. As far as the comic itself, there are those who can justifiably get confused between the many variants of each character running around.
The series itself, while pretty accessible, was being set-up by literally all of his previous Marvel work, and the original Secret Wars. Marvel seems to have understood this and published a Prelude to Secret Wars trade collecting relevant issues of Secret Wars and Hickman's works.
Draco in Leather Pants: A number of people have been of the idea that Doctor Doom is the real hero of Secret Wars, having killed the Beyonders and saved what's left as Battleworld and the only reason people are going against Doctor Doom is because "he's Doctor Doom and thus, he's bad and shouldn't be in control". This is despite the fact that he actively suppresses people's memories, sends his Thors out to kill people who don't bow down and kiss his butt and literally commands everyone to fight to the death in their worlds just because they might have crossed him wrong one random Sunday in September.
Ensemble Dark Horse: Faiza Hussein in Captain Britain and the Mighty Defenders. From her accidental Dynamic Entry to her Single-Stroke Battle with Big Boss Maria Hill, fans just loved her and were quite disappointed when it turned out the series was only two issues long.
Fan Nickname: Annie Parker's gotten two - "Menace", due to her Badass Boast as she pummels the Sinister Six, and "Anime Parker", when some fans realized saying her full name, Annie May, real fast leads to that. The former is endearing, the latter is derogatory.
Fanon Discontinuity: For some odd reason, the Marvel Comics Wikia treats the Spider-Girl back-up stories not as a continuation of Mayday's story post-Spider-Verse, but as another part of the whole Secret Wars saga. This is despite the fact that Web Warriors features Mayday as a main character and sporting the costume she dons at the end of her back-ups.
Harsher in Hindsight: The Captain Britain and the Mighty Defenders and its version of Toni Ho shows her as having a loving relationship with her father. Then during her appearances in New Avengers (2015), the mainstream reality's version is shown to be angry at the mere mention of her long deceased dad.
Jerkass Woobie: Elsa Bloodstone in Marvel Zombies. Her upbringing and tutelage under her father was Good is Not Nice taken to the furthest extreme, which both explains her present attitude and makes her treatment of Shut Up seem almost warm and fuzzy by comparison.
Karl Kaufman, the Phantom Eagle. Sure he experienced the horrors of World War 1 and his original plan to present himself as a hero during that time blew up in his face, but feeling like he was 'owed' something for his struggles really shows that he's kind of a jackass.
Just Here for Godzilla: Some fans tuned in simply to check out the absolutely insane shit that happened during the event, like Captain America and Devil Dinosaur fighting an army of Hulks.
Loki: Well, I was exaggerating. Dramatic effect. How'd you know?
The final issue of Captain America And the Mighty Avengers has a similar scene, where Dave laments that the world is about to end, only for Luke to state that he thinks this isn't really the end.
Luke Cage: Just the end of the chapter, man. Wait and see what comes next.
Spider-Man: Renew Your Vows is being advertised as the last Spider-Man story ever. Yeah, sure.
The first issue of the event is essentially a massacre but given the premise of the series, a lot of people have to come Back from the Dead to fight on Battleworld. Doom also saved the New Yorks of both the marvel and Ultimate Marvel universes, along with all their local heroes, before the explosion; and merged them into a single domain in Ultimate End.
For a lot of fans, Marvel's bragging of a "smaller" multiverse. The entire problem here is that there's really no way to "destroy" a universe in a way that sticks, just like a character. Case in point, many universes have been professed to be "destroyed" at some point or another (for example, the Age of Apocalypse reality) but still showed up later at some point or another. And then there's books like Exiles and Spider-Verse, where a vast multiverse is the whole draw. Like Joe Quesada and Dan Didio both saying "Dead means dead" years ago, good luck making this stick.
Alas, as predicted, everything is more or less back to normal. Even the multiverse is being rebuilt by Franklin Richards.
Issue 8 has Doctor Doom casually killing Thanos, who is one of Marvel's largest villains. It didn't take long for solicits to reveal Thanos' return.
The three week-old hamburger that changed the Marvel universeExplanation (spoilers) Miles gives Molecule Man a burger he had in his pocket when he hitched a ride on one of the Life Rafts, to which Owen, who is being used as Doom's power battery, says he's in Miles's debt, which he repays by placing Miles and his family on Earth-616 when the multiverse is restored. While already quite funny, the fact that the burger was three weeks old (technically eight years, three weeks, but it was in suspended animation along with Miles for those eight years), plus Miles and Peter's hilarious argument about giving a man an old hamburger, has cemented it in people's memory.
Narm: Issue #4 of the main series opens with Thanos battling multiple Thors, which would be an awesome scene... if not for an incredibly silly look on his face.
Nightmare Fuel: The initial premise of the story is what happens when the greatest superheroes of two worlds come together to prevent a universal apocalypse... And they find out that there is nothing that they can do to stop it.
Shocking Moments: Just the announcements alone are chock full of Cool Versus Awesome scenarios: from a post-apocalyptic gladiator Captain America riding on Devil Dinosaur to fight Hulks, to golden age World War 1 fighter pilots battling dinosaurs in the skies, to a death race formed from dozens of Ghost Riders across time and space, a legion of Thors joining together to solve Space-Crime, Zombie Superheroes against killer robots and so on. Even the core concept of the event, all the remaining universes in the comics multiverse being smashed together and forced to fight to the death in Battleworld, is pretty high in the awesome itself.
The entire final battle outside Doom’s castle in the main series, which keeps one-upping itself with the crazy stuff that keeps entering the fray. It started off as a Curb-Stomp Battle between Maximus’ followers and Doom’s armies, and soon devolves into a battle royale involving Hulks, Thors, The Thing, Galactus and at 2 Physical Gods.
They Changed It, Now It Sucks!: While fans love Bendis' Old Man Logan series, the one sticking point seems to be his portrayal of Logan's healing factor. In the original Old Man Logan story, Logan's healing factor had been slowed by his aging. It took him over two days to fully heal a bullet wound! In Bendis' series, it's back to what mainstream Wolverine has. This is less a problem within the actual series and more to do with the fact that Old Man Logan is confirmed to become a Canon Immigrant, and many readers were hoping he'd have a dialed-back healing factor to avoid the problems the original Wolverine had as a character.
Ultimate End, which was marketed as the Grand Finale of the Ultimate Marvel universe, ended up being a storyline of 616 and Ultimate characters interacting with one another. This led to some fans who had been invested in a decade's worth of Ultimate storylines feeling cheated.
Several of the universes chosen for territories were barely glanced over, such as New Quack City and Egyptia. New Warriors fans were especially bitter about the later since the only story that took place there focused on the X-Men.
Too Cool to Live: The Frank Castle shown in Battleworld volume 1. He is Frank Castle with the magical powers of Doctor Strange, and is shown to effortlessly kill a Hulk, Ghost Rider and Spider-Man in a matter of seconds and has an open hatred for Doom, leading you to believe he could be a major threat to Doom's Empire... except he simply lets Wolverine kill him instead for no apparent reason. Even stranger considering Frank's usually a stubborn Determinator.
Many people were wondering if the zombies had a leader and if so who it was, they probably were not expecting it to be Magneto, considering he was never even infected in the original story.
Aside from a very brief cameo in 2008, Weirdworld had neither been seen or even mentioned since 1982.
The original Days of Future Past back in 1980 mentioned Colossus and Kitty Pryde having children who all died, and have never been mentioned again by Marvel since then. Years of Future Past features a daughter and son of the couple as main characters.
And that's not even getting into all the stuff Jonathan Hickman's wrote setting up Secret Wars. Even hardcore collectors have their work cut out for them with this one.