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.
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.
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.
Ensemble Darkhorse: Even those who disliked Costa's run seemed to like the Character Development he gave Thundercracker, continuing what Shane McCarthy started in Transformers: All Hail Megatron and actually utilizing Thundercracker's bio for the first time in forever. 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.
It Gets Better: 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.
Like You Would Really Do It: Ironhide get's killed people even counted the days to when he'd come back, and no one was that surprised when a Miniseries was made about him coming back to life.
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.
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.
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.