Author's Saving Throw: Arcee's origins as a formerly genderless being made female against her will as well as being psychotically obsessed with killing Decepticons didn't sit well with a lot of fans. In response to the backlash, it was subsequently established that natural female Transformers existed. It's particularly telling that when Windblade's self-titled miniseries was announced, writer Mairghread Scott made it clear that Windblade was always female and wasn't made that way because of experimentation done without her consent.
There's the Movie-inspired Artwork which people think is good because of the detail, or just creepy and bad.
The first arc, too predictable and cliche, or a big risk with Ironhide's death and awesome appearance of Menasor.
The International Incident Arc: Some fans praise the non-movie art work, some find the story lacking, others find the Unfortunate Implications uncomfortable.
The Revenge of The Decepticons Arc. Some fans see it as the point where the series Grew the Beard, Milne's movie artwork was better received, it saw the return of the main Decepticon forces as well as Megatron taking a level in badass and the storyline made for a better paced gripping race. It's detractors feel that Megatron's return to form abuses The Worf Effect and the ways he keep winning (including defeating Optimus and then surrendering) turned him into a borderline Villain Sue, despite their return, the other Decepticons are barely players, finally Megatron now feels that Humanity is his true Worthy Opponent and goes out of his way to involve them.
Chaos: Is the artwork breathtakingly beautiful, or really hard to make out.
The humans as transformer killing antagonists. Some think it's a great spin, to make the Human's competent, others think it distracts from the Transformers themselves. This isn't helped by Spike and several others extreme unlikability.
Rodimus in issue 13. He singlehandedly infiltrates/partially destroys a Decepticon base and defeats several Decepticons, including Starscream, just by acting like a psychotic badass. Only a crazy awesome person can beat a bad guy by SHOOTING THE MATRIX.
Creator's Pet: This run was the start of Bumblebee completely swallowing the plot in IDW's Transformers continuity. For one thing he takes over leadership of the Autobots in the first arc and gets praise from a bunch of Autobots despite being an abysmal leader. Even worse is that this was actually enforced by Hasbro; Mike Costa wanted to kill Bumblebee off in the first issue but the execs refused and made him give Bee a spotlight.
Critical Backlash: The fans who hate this run on the series are so vocal about it, that some fans who go into it expecting a disaster, walk away seeing it as a decent, if flawed, comic.
The Autobots are an unwanted, uninvited occupying force that are also fractious and unable to effectively deal with conspiracies that happen right under their noses. Those of them that are sympathetic are kept from being able to do anything until it's too late.
Skywatch is made up of trigger-happy,loose-cannons who work to conceal their activities from the world at large. Earth's Children is composed of irresponsible, violent, ungrateful radicals who target all Transformers indiscriminately.
The Decepticons are marauding sociopaths railing against a social system that no longer exists and enemies that are not actively attacking them.
Dork Age: The sheer amount of Broken Base and revile that this run gets pretty cements it as this.
Additionally, many are fond of Bob the Insecticon, Sunstreaker's spiky yet strangely adorable pet and helper-dog and Garnak, the lovable oaf alien who joins up with the Autobots during the "Space Opera" arc and becomes The Lancer to Rodimus.
Foe Yay Between Megatron and Optimus, especially during Prelude to Chaos. In spades. The two talk about previous battles like old friends, Optimus is desperate to convince Megatron to change and their first conversation even ends with them chuckling about past encounters. Megatron even thanks Prime for saving his life the first time he met him, an encounter that he'd previously pretended not to even remember. Heck Rodimus actually lampshades it, commenting that their conversation was getting awfully cozy for a pair of arch-enemies.
Mis-blamed: As much as Costa is reviled for making Bumblebee suffer of Designated Hero syndrome, among other problems, his original intention was to have him killed, but was vetoed by Hasbro.
Rewatch Bonus: Once you've read the Police Action story arc and know the revelations concerning Spike and Swindle, you may notice a bunch of hints and foreshadowing in previous issues. Not to mention it puts all of Spike's dialogue in a whole new light, especially in scenes where Spike is talking to the Generals.
Slow Paced Beginning: The first story arc has a lot of pacing issues, Padding, and is over-all not very interesting for the most part. But once you get past that the pacing gets much better and the quality of the storylines jump drastically once you reach the "Revenge Of The Decepticons" story arc.
Strawman Has a Point: Jazz killing John Powell. The other Autobots act like he crossed the line but as Jazz rightfully points out, he only did it because Powell was a psycho who was about to murder a group of wounded Autobots in cold blood. Both here and later in Robots In Disguise it's shown that while Jazz does regret it came to that, he doesn't exactly feel remorse over killing a guy who was trying to murder his friends.
Specifically, North Korea would use the evil Alien Robots who just invaded the planet a few years ago and caused chaos and death on a large scale, to invade and expand their territory. The Chinese would also use these invaders, though only for defense purposes it seems, despite the fact that some other Decepticons leveled Bejing and killed everyone there. America would team up with the invaders who say they're good, and hide their actions from the rest of the world note Kinda, Skywatch had gone rogue, and one of the members, Sandra, told the rest of the world. Also, Russia's solution to all of this, shoot a nuke at the North Korean Chinese border before any country can object.
As noted in this article, "Spotlight: Arcee" has disturbingly transphobic implications with Arcee being established as initially genderless and made female against her will as well as the trauma of the procedure making her violent and psychotic.
What an Idiot: In Arc 1: Rodimus and his group work with the Decepticons to get off planet, suspicious as it is. They're also lead by Swindle, well known intergalactic Con-Man, smooth-talker, and... named Swindle. While the Autobots can be forgiven about Menasor, only the audience saw him coming to the shock of no one but these Autobots, Swindle's deceived them, who knew? Not Prowl's finest moment. At least Magnus has the good sense to try and arrest him on the spot, and Rodimus's group is only the minority.