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.
Adaptation Displacement: Sort of. The comics came out several months before the first episode of the cartoon, but the cartoon's the one that gets referenced constantly in every other piece of media.
Anticlimax: The comic ended on one due to Marvel cutting it short over declining sales. There was supposed to be a proper finale storyline involving the Autobots going on a journey to find the Last Autobot whilst dealing with the Decepticons and Galvatron but Furman was forced to condense it into about four or five issues. Thus the war ends after a single battle on Klo, Galvatron is defeated by being tossed into a lake, the Last Autobot is found in two issues flat, and Megatron, Starscream, Shockwave, and Ratchet are killed off before their storylines can be warped up. Subverted now thanks to Regeneration One, which is essentially giving the comic its' proper conclusion.
God-Mode Sue: Circuit Breaker. Being a Poorly Disguised Pilot designed by the writer Budiansky as a fallback career, most of her Budiansky appearances are about establishing how awesome Circuit Breaker is while using the titular Transformers as punching bags.
Circuit Breaker only fits as a God-Mode Sue physically. In pretty much all her appearances, she's shown to be so irrational about Transformers (admittedly, she's been through a seriously traumatic event due to Shockwave - she definitely has PTSD) that she almost always makes the situation worse.
Hilarious in Hindsight: The original plan for the last storyline was going to be the Autobots going on a quest to find the Last Autobot, an ancient and legendary mythic being. Years later Transformers: More Than Meets The Eye, while in a different continuity and with a different focus (the Knights Of Cybertron) has this idea as it's basic premise; a crew of Autobots go off on a quest to find an ancient legend.
Idiot Plot: For the last issue of the Underbase Saga. So Optimus has known all along from his past experience that the whole Underbase would be too much for a Transformer to harness, that it would get itself killed trying to absorb all of its enormous power? So when they find Starscream already in the process of absorbing it, shouldn't Optimus have, oh, just let him absorb it all and blow up instead of stopping the process by shooting him out of its way when he has already absorbed enough to be undefeatable, and having the Bots and Cons go after him resulting in a good deal of them getting killed while he constructs a rocket with reflectors to bring back the remaining Underbase and have it finish what it has started with 'Screamer?!?note The fact that he immediately chooses to construct the rocket to bring back the Underbase so that Starscream can absorb the rest of it, as well as the confidence he has in his actions, shows that for him it isn't a final gambit; he knows that this is THE solution all along!
Seasonal Rot: The Budiansky issues start off okay, but soon degrade into nonsense.
They Wasted a Perfectly Good Line Art: John Ridgway's black and white art in the UK comic is very detailed and realistic. About half the pages had colour added in the original release, and they were all completely recoloured for the American re-release; in both cases, the colour took out a lot of what made it impressive.
They Wasted a Perfectly Good Plot: Grimlock as Autobot leader seemed a fantastic concept, especially with an introductory story of him learning to respect humans and that a good leader needs more than strength. He promptly develops Aesop Amnesia and turns into The Caligula, sitting on a throne wearing a crown, beating up his troops and showing no interest in fighting Decepticons. Incredibly, the only one bothered enough to stand up to him is Blaster and just as the storyline builds to a confrontation between them, all the Earthbound Autobots disappear for four issues (during which Blaster was left stuffed in a cupboard and forgotten by everyone). There's a one issue wrap up where the delayed confrontation is interrupted by a Decepticon attack, then they all disappear for another four issues by which time Optimus Prime's back and the whole storyline's forgotten.
Optimus Prime's first death should be a dramatic moment. He's sacrificed his morals simply to win a temporary advantage in battle, and rather than live with the knowledge that he did that, allows himself to be killed, regardless of the bad position it will leave his troops in. It's just too bad he allows himself to die over cheating in a video game.
Took A Level In Jerkass: This happens A LOT in this series, but its especially bad for Skyfire and the Dinobots. Even SWOOP manages to become an arrogant douchebag here, despite being the sweetest character, arguably, in the entire cartoon.