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: Skywarp claims to have killed every single person in Beijing. Given Beijing's massive population, the short timeframe he claims to have killed them in, and the fact that Skywarp has never been portrayed as so dangerous and skilled, some readers interpret this as Skywarp lying to make himself look cool. Not only would this be completely in-character for Skywarp but he makes this claim to Bombshell, whom he was clearly established as being jealous of.
Base Breaker: The series itself, which moved away from Simon Furman's ongoing cosmic storyline in the hope that a change in story direction would help stop the trend of continually falling sales. Sales leveled out and stabilized, so from that perspective the series accomplished its goals. However, it quickly became extremely controversial, with some fans very unhappy about dropped plot elements from Simon Furman's run on the book as well as the reversion to older designs for some characters.
The current editor of Transformers, Andy Schmidt, said that the decline in sales over the course of the 'ations wasn't as great as previous editors had hinted at and used to justify the switch, so all the switch to AHM managed to achieve was replacing readers they lost because of the switch to AHM, making their previous readers unhappy in the process.
Franchise Original Sin: There were some complaints about the human characters in the comic, with Spike in particular being somewhat disliked. However it wasn't too much of a problem and Sparkplug gets some great character development in this comic. Come the next ongoing however, and all the problems that the human characters had (being jerks to the Autobots, complaining, getting more screen time than the main characters, etc.) were amped Up to Eleven and Spike and Sparkplug were changed into The Scrappy overnight.
Hilarious in Hindsight / "Funny Aneurysm" Moment: When Drift was hyped and during his debut, he was the butt of many Poochie jokes, including the classic "Whenever Drift isn't on panel, the other characters must ask 'Where's Drift?'". In issue 7, that exact scenario happens. It happens again the next issue, too.
In a flashback we see that Ironhide doubted Brainstorm would live through the war. Come More Than Meets The Eye and Robots In Disguise, and not only did Brainstorm survive the war, he was one of the few who lived through it from beginning to end.
Hype Backlash: Much of the anti-Drift sentiment was in response to the "He's awesome and you're gonna love him" shilling.
Memetic Mutation: The solicitation for issue 15 claimed the issue would show why Perceptor "rejected science and took up snipering", the odd choice of word (the proper term is "sniping") led to a running gag in the fandom that Perceptor was not a sniper, but a sniperer, culminating in this hilarious fancomic◊ that explains it all.
Ironhide punches everyone! note Explanation: Ironhide punches a lot of people in the story. TFWiki.net fell in love with this and made it a minor Running Gag.
Moral Event Horizon: The events of this series could be considered one big horizon crossing moment for Megatron, especially what he had Bombshell do to Hunter.
The whole idea of the Decepticons ruling the Earth is woefully unexplored given the awesome potential there for a terrifying and dramatic story. This is at least partially due to Executive Meddling from Hasbro that prevented Shane Mc Carthy from showing more scenes of the Decepticons taking over.
Sideswipe mercy killing Hunter had loads of potential for a character arc, but nothing came of it. This isn't really McCarthy's fault, since it was later writers who decided to not follow up on this.
What an Idiot: Hook doesn't know who Frenzy is, despite the two of them being some of the first Decepticons (Rumble and Frenzy are the first to sign up with Megatron). Skywarp chalks this up to Hook being the new guy, despite Hook being a Decepticon longer than him.