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.
Alternate Character Interpretation: Ultra Magnus giving Prowl the Data Slug and telling him not to destroy it. Magnus's face is obscured by shadows when he says he trusts him. Did he trust Prowl to do the right thing? Did he give it to Prowl to absolve himself of the moral dilemma of the drive, having prior knowledge of its lurid contents? Or did he give it to Prowl knowing full well that the secrets of the Autobots would be better left undiscovered, and Prowl was the best man for the job?
Breakout Character: Ironfist. Since the series started, he's gotten himself two new figures (though they're both exclusives), incarnations in the Transformers Animated and Transformers Prime universes, his counterpart in Wings of Honor turned out to be Not Quite Dead, and he even got himself a cameo in Shadowplay, years after his last appearance in Wreckers. James Roberts admits in an interview that he somewhat regrets killing Ironfist... which, when you consider Roberts's reputation, is quite a compliment.
Prowl as well.
Breakthrough Hit: Nick Roche had already worked for IDW, and this was James Roberts' first work. Both instantly became fan favorites and are pretty much the equivalent of A-Listers in the fandom now.
Complete Monster: Overlord is probably the perfect example of the Complete Monster trope in Transformers fiction. He's one of the most powerful Decepticons but unlike the others he doesn't give a damn about the cause, or conquest, or even defeating the Autobots. He just wants to kill anything and everything he can, in as many sick and twisted ways as possible. He horrifies all Cybertronians, Autobot and Decepticon alike, and Megatron was wary of him that he had Shockwave alter his brain so that Overlord could never beat him. When he took over Garrus 9, he essentially turned it into a cross between a concentration camp and a gladiatorial arena, with torture, murder, and prisoners being forced to fight to the death for his own sick amusement. Nothing any other Transformers villain has done really compares to the pure evil that Overlord is guilty of.
Designated Villain: It's revealed through the comic and various side-materials that, Squadron X was this in-universe. They weren't engaged in any sort of violence at the time the Wreckers battled them on Pova (they were just performing some refueling and munitions transportation), the Wreckers started the fights and rivalry with them, most of the team were noble demons (Ferak was planning to retire and Earthquake was going to be either kicked out or executed due to suspicions that he was about to pull a Heel-Face Turn), poor Fang was only a jerk because Impactor maimed his voicebox and left him unable to speak, Triton was forced to join against his will, and Crosscut was only considered a threat because people kept mistaking him for someone else who actually was evil. In fact, if the backstory provided in "Zero Point" is anything to go by, the Wreckers are bigger monsters than Squadron X ever was.
Evil Is Sexy: Overlord, with his handsome (for a giant robot) looks and charismatic, almost theatrical mannerisms. Doesn't make him any less scary or creepy, however.
Fashion-Victim Villain: Subverted, characters up to and including the infamous Skyquake have sane colors. That said, the Predators are still a little garish - Snare's bio notes that this is for camouflage on the strange worlds they've been stationed on in the past.
Fridge Horror: As pointed out by James Roberts, in the epilogue Prowl never bothers asking about the fates of the Autobot prisoners who were the alleged reason the Wreckers were sent to G9 in the first place. In other words, either he didn't care or he was hoping the prisoners would be dead.
Hilariousin Hindsight: Rotorstorm's "Wreckers, combine!" joke is a lot funnier given that an actual Wreckers combiner team (being redecos of the Fall of Cybertron Combaticons) was released in 2013... though it sadly doesn't include Rotorstorm.
Ho Yay: In "Bullets," it's fairly easy to read First Aid's encounter with Springer as this.
Moral Event Horizon: Impactor's deeds at Pova, toIronfist. These included executing Squadron X, while they were chained and on their knees. It's left up to the reader to decide whether Impactor was justified or not. He becomes much less justified after the backstory for Squadron X was revealed later on (see Designated Villain above).
This series could be considered one big horizon crossing moment for Overlord... though if supplementary materials and character reactions are to be believed, he's done even worse things than this before.
Stalker torturing Impactor, Springer, and Twin Twist which ends up resulting in the Jumpstarters' deaths.
Skyfall actually crossed it before the story even began, but you won't realize until the end.
Running the Asylum: A well-received example. The authors are both Promoted Fanboys, and the series follows a Transformers-exclusive iteration of a rule detailed on the Running the Asylum trope pages: the characters used as OC Stand Ins were available in the UK as toys around the time that the authors were younger, which explains their motivation for rescuing them from eternal obscurity.