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  • Broken Base:
  • Captain Obvious Reveal: The bartender of the C.D. Pub being Megatron. While no one suspected his true identity during his first appearance, the bartender's name was not spoken until the Season 1 finale, and Megatron continued to appear only in shadow even after he was shown in lighting good enough to reveal his design. In fact, because of the way the dialogue is arranged, Megatron's reply to his name being spoken can be viewed as a Lampshade Hanging on the matter.
    Megatron: Like there was any doubt.
    • Artillery being the daughter of Megatron. Even ignoring their many intentionally shared traits and the various hints dropped beforehand, the two had this relationship in so many prior fan series that readers were casually referring to the two as family in comments a full season before the reveal happened.
  • The Chris Carter Effect: One of the major complaints about the series. Due to the high number of characters, the series features a large amount of subplots. However, this also means that when said characters are Out of Focus for long stretches of time, their plots are put on hold as well. As such, some feel that the series will spiral out of control and be unable to resolve all these plots. The fact that this is what happened to both versions of Stonecrusher's previous series, Trabsformers Nexus, doesn't help aleviate these concerns.
  • Crack Pairing:
    • As Autobot Academy takes characters from all Transformers series available, and doesn't shy away from pairing them up, several canon examples were bound to happen. These include:
      • Bomb-Burst x Roulette. The one time these two appeared in the same continuity was during the IDW comics, and even then they never came close to interacting.note  Even Stonecrusher is baffled by this particular pairing.
      • Offroad x Plug and Stampy x Plug. Not only is the canon version of Plug a Toyline-Exclusive Character, but from a toyline that's not even in the same universe as the other two.
      • Tap-Out x Stiletto is another example of two characters who never appeared together in canon.
      • Most families being Related in the Adaptation resulted in many of these for parents who both weren't original characters, including Lunaclub x Needlenose, Discharge x Artfire, and Blood x Ether Walker.
    • For a noncanon example, Stonecrusher was once asked for his thoughts on Offroad x "Goldknuckle". The characters have never interacted once.
  • Fridge Horror: Artillery suggesting that Beta Maxx use time travel to kill Megatron as a sparkling to prevent the Siege of Acadeimos from happening initially just looks her typical Anti-Hero attitude... until one remembers that she just got confirmation she's Megatrons daughter. That means she's advocating for a plan guaranteed to kill her in the process and erase everything she ever accomplished, and she doesn't seem at all concerned by that fact, even calling Beta Maxx a coward for rejecting the idea outright.
  • Harsher in Hindsight: When originally presented, Nautica spending all her time in a workshop to the point of falling asleep while working and trying to get out of attempts to be more social was simply a result of her having No Social Skills, with the people making her meet others simply resorting to more forceful means of helping her overcome this flaw. Then it's revealed Nautica was forced to infiltrate Autobot Academy by her horribly abusive father and build him a set of Powered Armor with the advanced technology there. Now it's clear that what looked like Nautica being an extreme shut-in that would rather spend all her time in a lab were the result of her being forced to keep working on building weapons and gadgets and to ensure nothing and no one got in the way of her work, and that the well-meaning efforts of others to try and help make her more social were putting them in danger for interfering with Nautica's work.
  • I Knew It!: Readers were guessing that "Mini" is actually Delta Magnus nearly ten months prior to the reveal.
  • Unexpected Character: It was a surprise when Ruy-Han, a character who appeared in a portion of the Roleplay generally ignored by the comic, showed up in "Field of Scientific Minds".
  • Unintentionally Sympathetic: Circuit isn't a good guy, but the punishments he receives are rather extreme. Notably, he gets shot in the foot by Longshot when simply talking to Aranea, and this is before he tries to trick her out of some of her money. He also gets insulted when he's trying to do the right thing, but can't simply because of outside circumstances.
  • Unintentionally Unsympathetic: Longshot. He complains about everyone hating him, but a lot of this seems to be his own fault. He didn't do homework because he was confident that he already knew the material and he's shown purposely testing Fortress Maximus' patience just to see how far he can go, which indicates his teachers had good reasons for not liking him. Plus, Longshot admits that he generalizes people, which makes his claim of being the Only Sane Man at school doubtable, since he just seems to judge everyone he meets by whatever trait they display upon first meeting them. His treatment of Circuit is rather extreme, especially considering it starts before he finds out about his less savory traits, and his distrust of him can reach ridiculous extremes, most notably when accusing Circuit of sneaking around the school at night to get into trouble in the middle of a potential Decepticon attack that Longshot was in the middle of investigating. There's also him shooting Circuit's foot for talking to his crush Aranea, which makes him come off as a Crazy Jealous Guy. All in all, Circuit's "The Reason You Suck" Speech to Longshot in "Nighttime Duel" is rather accurate.
  • Wangst: Longshot is rather extreme about how much people dislike him, but it's especially bad during his angry rant at the diner that ends with him yelling at another student that they don't know what he's going through and that they should shut up.

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