Acceptable Targets: Fred is the butt of countless fat-jokes, though he does prove to not be entirely useless.
Big-Lipped Alligator Moment: The weird time travel/alternate timeline hopping. Happens with no apparent cause, is never mentioned again.
Broken Base: Fans of the anime vs. the comic. The main points of contention are the kids all but disappearing from the story once Simon Furman took over, as well as the use of G1 Decepticons as Unicron's heralds rather than characters from the Armada toyline.
Ensemble Darkhorse: This show's version of Starscream. People thought it was a nice change of formula to make him a Noble Demon instead of, well, The Starscream. Alexis is generally the more tolerable of the human characters since she plays a big role in his character arc.
Epileptic Trees: There are a couple characters called Sideways throughout the multiverse, and it's definitely been speculated that they're all the same guy.
Ethnic Scrappy: Carlos. Though to be fair the "scrappy" status is shared by all humans in the series, as is usual for this franchise.
Foe Yay: Every scene between Megatron and Optimus makes the war sound like a lover's quarrel as well as their overwhelming obsession with each other. Hotshot and Sideways have their moments as well, along with Starscream and Jetfire.
Specifically, once the kids got Demoted to Extra and the show started focusing on the Transformers (specifically Starscream and Hotshot) fan response turned positive.
Hilarious in Hindsight: The little-elaborated-on Overload seems to be a Mini-Con piloting a transformable trailer, Headmasters-style. In Japan, Overload was named "Ultra Magnus" for some reason, and eventually got an Ultra Magnus-themed redeco in the West. Come the IDW Transformers comics, and Ultra Magnus is revealed to be a suit of armor piloted by a Minicon-sized Transformer aptly named Minimus Ambus.
Tons of this with Hotshot and Red Alert and the dialog between Jetfire and Optimus when they're talking about what they used to do and the whole scene where they are explaining why they can link-up after and during the battle with (mainly) Starscream is rife with suggestion, especially when Optimus says its been awhile since they had done it.
Demolisher practically melts when Megatron takes a hit for him and says when Demolisher expresses concern and I quote Megatron "It doesn't matter as long as you're alright". It was an act on Megs' side but Demolisher is viewed as being one hundred and ten percent gay for Megatron.
Just Here for Godzilla: The Armada comic is mostly known for the admittedly epic clash between Armada Megatron and G1 Galvatron, acting as Unicron's herald.
Special Effects Failure: The show is infamous (though not to the degree of Transformers Generation 1) for its ropy, often episode-breaking animation quality, especially during its first half. Characters are often miscolored, badly proportioned, and for several scenes in the episode "Decisive Battle"note considered the worst looking episode of the series, Starscream is represented as nothing but a floating black dot with wings◊! Robot animation in the first few episodes often amounted to static drawings sliding across the scene. At times, you can barely tell what's going on because the animation is just nuts.
The very liberal use of Photoshop filters for the visual effects. It's easy to tell that those eyecatches of Optimus and Megatron had the metallic effect used on them, and it looks awful◊.
The Scrappy: Alexis is somewhat less hated due to her role in Starscream's character arc but the others are largely despised. The kids scrappydom is likely the reason why Simon Furman chose to pretend they didn't exist once he began writing the Armada comic around Issue #6. The one comic that focused on the kids, prior to Furman taking over writing duties, is widely considered the worst issue of the entire run.
To a lesser extent, the show as a whole. While still hated in some circles, its contributions to the Transformers mythos and unique takes on certain characters have caused many to reevaluate it as a passable, if flawed effort. Its successor managing to be even worse than Armada's weakest moments also helped.