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: Did Phaeton ever truly care about helping his fellow Neosapiens, and was he ever truly The Atoner for what he did at the end of the first rebellion, or was he just an evil, power mad tyrant manipulating everyone to further his own ambitions?
General Draconis. From his death camps on Venus, starving the populace, to being personally responsible for Nara's parents deaths. Genocide, betrayal, nothing is too much for him. He even betrayed Phaeton when he was relatively sane, and was about to kill Thrax, an honorable Neosapien Warrior who wouldn't kill civilians.note The incident with Thrax deserves an explanation. Thrax was a disgrace because he had spared a member of Exosquad after beating him fair and square. Draconis gave Thrax the chance to "redeem" himself by ordering him to activate a huge bomb in the heart of a city full of civilians. At the last moment Thrax destroyed the activation key and returned, claiming that the humans had disarmed it before the countdown had finished. What Draconis didn't tell Thrax was that the bomb didn't have a countdown; if Thrax had used the activation key it would have blown up immediately and killed him. That's how Draconis knew Thrax had disobeyed his orders — he came back alive. Draconis is so bad that even Phaeton, who is based on Hitler, doesn't seem as bad at first. Of course, Phaeton eventually surpasses Draconis' evil after going insane from Automutation Syndrome.
Phaeton, the ruler of Neo-Sapien empire. He uses words like "equality" and pretends to care about the well being and future of the Neo-Sapiens, but his actions prove this is nothing more than manipulative rhetoric. Before the series start, Phaeton sold out the Neo-Sapien rebellion to save his own skin, and rises to power by initiating genocide on humanity, establishing death camps and killing any who resist-and even those who don't. His tactics include forcible starvation, forced labor or just nasty executions. Not even his own men are exempt. Phaeton is very keen on executing them for minor failures and cloning them. Phaeton's ego and hypocrisy are manifest in how he sends so many of his loyal men to their own deaths on suicidal missions and at the end, even his most loyal aide Livia deserts him for his plans that would have wiped out his own race to secure his own victory. If Phaeton ever held noble ideals, they're gone by the time he enacts his plan at the start of the series and he grows more and more evil and he degrades physically and mentally. He is nothing more than a murderous, power hungry coward by the end and one who would see the entire galaxy burn for the sake of his own power and advancement.
Dr.Albrecht Ketzer turned an entire village of natives in the Amazon and himself into half-plant monstrosities, turned Medusa into a half-plant/half-Neo-Sapien freak, and injected Nara Burns with the same serum. He views her only as an experiment, and wanted to kill all the humans AND Neo-Sapiens in the nearby city.
Foe Yay: Even though he's asexual, Phaeton seems to spend a lot of time obsessing over Marsh. Some of his interactions with Marsala have quite a bit of Ho Yay as well.
Hilarious in Hindsight: The Executive Producer of the show once compared Exosquad to Gundam, noting that both invoked World War II campaigns. Several of the voice actors in Exosquad would go on to dub various Gundam series.
Nightmare Fuel: If you stop to think about it, quite a bit for a saturday morning cartoon. Aside from the normal carnage of war (shooting and explosions and what not), we see characters get exposed to hard vacuum, starved half to death, put in cargo containers and launched towards the sun, and the effects of the Graf Shield, which crushes starships (and their occupants) like soda cans. That's just the first season, by the way. The second season gets much worse.
They outright call what Draconis is doing to the humans a genocide.
Captain Marcus, for being an outright incompetent Hot-BloodedJerk Ass who consistently makes the wrong decisions by being overly aggressive and refuses to listen to others who point out flaws, earns a lot of fan-flack. Even his death, normally of the kind that would invoke Alas, Poor Scrappy, generally fails; most viewers only wished he'd gotten killed sooner, it probably would have been better for Exofleet if he had.
What an Idiot: Not putting Melee Weapons onto the Exoframes to deal with the Neo Warriors and Neo Lords, thus the Exoframes being mostly helpless whenever they get to Melee Range (This may be due to Executive Meddling).