Angst? What Angst?: By the end of the series Barnaby's relatively well-adjusted, for a guy who recently discovered his father figure and sponsor, Albert Maverick, murdered his parents, mind-raped him twice into forgetting about it, murdered his foster mother, brainwashed him and the rest of the heroes into believing Kotetsu was the one responsible, and manipulated him for his entire life so he'd become a hero. After all this comes to light, Maverick tries killing everyone without a single hint of remorse.
It's stated in The Rising that Barnaby is still dealing with the trauma of his past despite all outward appearances. It's just that he has Kotetsu to help him work through everything and has managed to grow a lot since they first became partners.
Awesomeness Withdrawal: Despite the show's popularity, it took seven years for a second season to be announced.
The Big Bad, Albert Maverick, is seemingly the kind and friendly benefactor of superheroes and the founder of Hero TV. In fact, he was the secret leader of the crime syndicate Ouroboros and was involved in their criminal activities. To make things easier for himself, he presented NEXT as marketable to gain them fans and create a superhero legacy, all the while hiding the fact that he is a NEXT himself whose power was Mind Rape. He would murder the parents of future hero Barnaby Brooks to mold the boy into his perfect pawn, rewriting his memories every time Barnaby got too close to the truth. When he realized Barnaby's partner Kotetsu was too close to the truth, he had Barnaby's mother figure Samantha murdered and framed Kotetsu, wiping the memories of everyone who knew his superhero identity. After this failed, he decides to wipe out his own kind and replace them with more easily controllable robots created by Rotwang. Once the doctor has outlived his usefulness to him Maverick decides to murder Rotwang after revealing himself as a NEXT. Finally, he puts a gun to Kaede's head and tries to use her as a hostage.
Epileptic Trees: There have been a few people suggesting Scarf Girl keeps turning up everywhere because she is either the Big Bad, involved with Ouroboros, a Fangirl for the heroes or she's just cursed with awful luck.
Kotetsu's idol worship of Mr Legend in general, but in particular his consumption of Mr. Legend's Hero Beer◊ becomes rather less cute and funny come Episode 16, where it's revealed that Mr Legend became an abusivealcoholic towards the end of his life.
Many fans had a habit of joking that Ivan would be the first to die... until Episode 11 rolled along, at which point the fandom changed its tune to, "OH FUCK IVAN BETTER NOT HAVE DIED." He didn't, but it certainly was a close one.
Along the same lines, Kotetsu's smartass remark about Lunatic having a glove on his face (and the fandom's subsequent adoption of "Palm-Face" as a Fan Nickname for him) has become really unfunny following the revelation in Episode 16 that the design is based on the handprint burn scar on Yuri's face, left there by his father when Yuri burned him to death.
In Episode 19, Barnaby says Kotetsu was among those people who the murderer in his memory changed into; Kotetsu jokingly replies that he didn't do it. Then one episode later, Kotetsu is framed for the murder of Barnaby's housekeeper, who is the closest thing Barnaby has to a family.
Barnaby nearly delivers a spinning kick to Kotetsu in Episode 23. It used to be a heartbreaking moment... until it was announced Yuri Lowenthal, aka Spinzaku himself, would be voicing Barnaby. Now it's hilarious.
There was a superhero called "Pepsiman" created by Pepsi in the 90s, and here we have a superheroine Blue Rose who advertises Pepsi.
In Episode 8, Kotetsu tells Ivan his power is great because he can just copy what someone looks like and use their power, though Ivan quickly clarifies that it doesn't work that way, he can only copy people's appearances. Later on in the series, Kaede is shown to be able to Power Copy.
In-universe, Origami Cyclone is the lowest ranked hero due to his Shapeshifting powers being completely useless for Hero TV. Of course, he wised up and used other means to fight.
Rock Bison is treated as a Butt-Monkey despite his powers. Before his fight with Jake Martinez, you could see that he's really ready to rumble and then, the scene cuts him to being utterly defeated.
A downplayed example (see Unpopular Popular Character) but Abridged Series edits of the series will often highlight how the universe is determined to tell Kotetsu he sucks and imply that people are in more danger with him there because of his habit of breaking things.
And to go with him, there's Ouro-Bunny - same idea, really - it's Barnaby's evil version, sometimes a Villainous Crossdresser.
Fans have become incredibly preoccupied with fried rice after they learned Barnaby had been practicing making it just for Kotetsu.
After learning that not only Barnaby and Karina, but even his own wife had a tsundere side that was revealed only towards him, the fandom has concluded that Kotetsu has a second NEXT power - drawing out the tsundere in those who're fond of him.
After Episode 19, Maverick. In his case, what doesn't help is the date rape allegory from that episode.
Jake Martinez, whose outfit can charitably be described as looking like a male hooker's. His creepy interactions with... everyone and generally creepy behavior, complete with tongue-wagging, giggling and perverse enjoyment of violence don't help.
Also Barnaby himself, who's often portrayed in fanart as being a raging Kotetsu fanboy in a manner similar to "Perverted Homura" from Puella Magi Madoka Magica (whom he is sometimes drawn as being dressed like).
Moral Event Horizon: For Maverick, it's having Samantha murdered. Of course he actually passed it twenty years ago when he killed Barnaby's parents, but the former is the first time we see his evil side for ourselves.
Narm: Barnaby's breakdown scream in the stinger of Episode 18 is more than a little hard to not laugh at, with facial distortion to rival anything seen in Code Geass.
No Yay: Maverick is really possessive of Barnaby; to the point of drugging him, mind-raping him several times and isolating him in his private mansion. Add in the Power Perversion Potential of having memory-altering NEXT powers and no amount of industrial strength Brain Bleach is ever gonna be enough.
Paranoia Fuel: What Maverick did to Barnaby may serve as this for anyone who has been raised by foster parents. The people who (apparently) loved and cared for you? They're Manipulative Bastards who only ever saw you as a tool to fulfill their own agendas. And while people in real life probably don't have Psychic Powers that enable them to rewrite memories, there are still plenty of ways to manipulate someone ever since childhood.
They Changed It, Now It Sucks!: When the series became available on Netflix, the corporate sponsor logos on the heroes' costumes were nixed. Fans were less than pleased. Part this is because the sponsor logos are plot relevant, and removing them creates a number of inconsistencies.
Despite setting up Lunatic as a very good rival to the main body of heroes, and giving him a sympathetic background... he never really does a whole lot. His clashes with the heroes are very rare over the course of the series, and it's easy to forget he ever existed by the time the series ends.
Antonio Lopez aka Rock Bison is the only hero who doesn't have much focus throughout the entire show. Asides from being Kotetsu's friend and being the Butt-Monkey, you know nothing about the guy unless you read the supplementary materials.
Episode 15 features Keith dealing with both a crush and personal insecurities stemming from his drop in the hero rankings. He doesn't get a Kotetsu lecture/pep talk why exactly?
On a broader level, the idea of turning heroism into a business/advertising stunt is never really explored in any detail.
Unintentionally Unsympathetic: Edward, seemingly meant to be seen as a Tragic Villain who let hatred consume him, becomes really hard to feel sorry for when his hatred is far from justifiable, blaming (and even trying to kill) his only friend for something that's almost entirely his fault. The fact is, Ivan's actions were perfectly understandable. Neither of them had ever seen real combat in their entire lives and now Edward is jumping into an extremely dangerous situation with total abandon. Most anyone in the man's position would have a hard time leaping into action, let alone when dealing with armed thugs.
What an Idiot!: Maverick's plan to dispose of Kotetsu. It would probably have been easy to call up Ouroboros and arrange a heroic hospitalization, where he could do a memory edit during a visit. Instead he opts for a flashy plan that requires mindwiping everyone who knows Kotetsu's identity and then plastering his name and face all over the news, even though the necessity of the disposal is because his twenty-year edits on Barnaby's memory started failing when exposed to contradicting information. He also forgets that Kotetsu has a family, who could potentially cause the same problem. Not to mention that wiping the name Kotetsu T. Kaburagi from every record everywhere is time-consuming, probably expensive (do men in black suits get paid by the hour?), and could still fail if, say, Antonio had a note in his jacket reminding him to pay Kotetsu back. Also, you're dealing with a hero who was sponsored by a different company before Maverick had him become Barnaby's sidekick and whose HeroTV file (complete with real name) was researched by a judge who, via his anti-hero persona, had confronted him numerous times. It's almost like how a Gambit Roulette would end if it was played out logically.
It's even dumber than that. Maverick had Kotetsu's complete trust when he decided to put his plan in motion. Kotetsu actually called him about the holes in the story, but instead of suspecting him, he came to the conclusion that some outside party was to blame. Maverick could've easily rolled with this by framing Ouroborous, who have little use to him at this point, being more of a liability than anything else. He didn't even need to mindwipe anybody!
After learning about Kriem's childhood it's hard not to feel sorry for her.
Yuri Petrov aka Lunatic is a cross of Stoic Woobie and Iron Woobie after we found out that his dad is Mr. Legend himself who slowly lose his powers and started abusing his wife and son instead. Then, Yuri had to kill his own dad in self-defense and his mom hated him for it, eventually slipping into insanity.