Broken Aesop: Some people think Ty'Veculus got a raw deal, since he is famously called out for dishonesty when he pretended to like an intentionally badly-designed new costume Stan gave him, and yet later he is eliminated because he was honest about who he felt should be eliminated rather than lying by offering himself up.
Broken Base: Monkey Woman's elimination in Season 1 will likely always have people divided between those who felt it was entirely deserved (given Monkey Woman's What an Idiot! mistake she'd made with giving out her real name to the waiter without having even been asked and having concealed that she'd had experience as an actress beforehand) and those who felt that, even if the reasoning for eliminating her was sound, it was unfair for Stan to forego the usual rules for elimination and not consider anyone else who'd made mistakes in that challenge for elimination, singling out Monkey Woman as the only viable option for elimination, meaning she was denied a fair chance.
Creator's Pet: Some fans thought that Hygiena was a lame superheroine that should not have gotten as far as she did in her season, but Stan Lee seemed to like her. A few thought the same of Fat Momma in the first season, so she was this to those for whom she wasn't an Ensemble Dark Horse.
Elimination Houdini: Hygiena. In the second-to-last episode, she revealed her home address to the TV personality and still made it to the finals out of sheer luck because Stan decided that nobody would be eliminated in the second-to-last episode, and that the finale would have three contestants instead of two.
The above-mentioned Fat Momma in-show. In one of the final episodes, the remaining three contestants had to convince an elementary school class to be inspired by their hero persona, and then the kids of the class had to stand behind their favorite. Fat Momma gave a Heartwarming speech about learning to love yourself for who you are, and more than half the class got behind her.
Game-Breaker: A late challenge in the second season involved bonding with children and using the knowledge they were taught in school to solve some puzzles. The guy who failed? Parthenon, who was a teacher, and therefore didn't need the children's help.
Hilarious in Hindsight: One of the season 1 contestants was a pink-and-black wearing, cellphone-themed superhero named "Cellphone Girl". Years later, in South Park: The Fractured but Whole, Wendy's superhero persona would be a pink-and-black-wearing, cell-phone themed superhero named "Call Girl".
Narm: Parthenon's catchphrase, "Who says diamonds are a girl's best friend?", is probably the most unsuperheroic and unimpressive Non Sequitur of a catchphrase that has ever been devised.
Shocking Elimination: Creature was eliminated for jaywalking, therefore breaking the law, during a challenge. Her justification (she didn't grow up around traffic lights and only learned to look both ways before crossing a street) didn't help, considering she also mentioned that superheroes have broken much worse laws.
Tear Jerker: In the convict challenge, Feedback asks his convict how he would feel if someone he was close to was killed. The convict opened up by saying his father was killed. Feedback, having lost his own father to suicide, tells the convict: "I don't know what your life was like. But I know what it's like to lose a dad. And I'm sorry." They then share a genuine hug.
Wangst: Fat Momma in Season 1, and Whip-Snap in Season 2, both teeter on the edge between angst and Wangst, especially Whip-Snap.
Whip-Snap's wangsting got her eliminated - Stan Lee's final speech to her basically said, "If you can't deal with your own problems, you have no business being a superhero on top of it." He ought to have made the obvious comparison to Spider-Man, noting that (at least when written well and not selling his soul to Satan to fix the problem for him) Peter Parker actually works to solve the problems amidst his superhero life, rather than crying about it every damn time.
Monkey Woman in Season 1 also had this problem: she was on the verge of tears every time something didn't go right for her. The interview she gave after being eliminated was filled with self-justification for why she shouldn't have been expected to be faithful to her superhero character persona because she's first and foremost "an actual person" and acting like she was a poor victim of unfair treatment.
They Wasted a Perfectly Good Character: Feedback's very detailed backstory and super powers did not transition into the comic book, which instead had them struck by lightning and subsequently using fairly generic electricity powers. It's been suggested that their original power of borrowing abilities from video games would have been a legal nightmare, which falls rather flat when there's no reason they couldn't have made up the games.
The Web Comic:
Hilarious in Hindsight: Vegeta and Piccolo's statements that Gotenks cannot be defeated by them due to his status as a fusion becomes hilarious in Dragon Ball Super, where in one of the filler arcs Gotenks fights off against a copy of Vegeta in his base form, and does nothing to him.