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.
"Distribution." You'll be guessing until the very end who's real and who isn't. And what in the name of Primus is going on. A 'simulation' that's a tournament-style matchup of every 'bot in the series, with robo-catgirl announcers. Some characters who are real walk in and out of things totally unconcerned with who's sitting across the room from them, seeing how they're usually trying to murder each other. Then turn out to not be real, making you wonder what the point of their being in the simulation was at all. Then whoever was just wondering if the guy who just walked out was or wasn't real... turns out to not be real. It was just... the most insanely random thing Transformers has ever done. Bad dubbing takes it from random to incomprehensible and insanely random.
In Superlink, this was a 500th Episode special for the entire franchise, was non-canon, and was shown at a special time. In the dub, to make up for cutting an episode, they added it to the actual run of the show. Right in the middle of a Darker and Edgier arc that was basically all-out war.
Dork Age: Beyond simply being regarded as an inferior sequel to Armada (by both the show's fans and detractors), it's regarded as the worst TF show period, due to wasted potential and very poor dubbing.
Demolishor retained this status from Armada prior to his reformatting, thanks to his conflicting loyalties between the both sides that he gained from living an era without the war, and losing that is considered to be one of the worst mistakes the show made.
Also, they tried to cut out Mirage's crush on Galvatron in the dub, but couldn't completely.
Mirage: But I've been so loyal! How could Galvatron not know how I feel about him?!
Padding: Unicron perishes in "Unicron Perishes," appropriately enough, but then it un-perishes so we can basically repeat the entire plot for 10 or so episodes. On a smaller level, see As You Know on the main page.
Much of the show is padded by re-using the Story Arc of trying to prevent Unicron's revival and then knocking him out before his body is destroyed.
Jerkass Woobie: The writers were clearly going for this with Kicker but it just made him even more insufferable.
Actually Alpha Q did call him out on his hypocrisy at least once, when he does the same thing he hated his father for.
Ironhide also qualifies, thanks to his rather stupid design, annoying voice, and near-This Loser Is You personality. Ironhide toys were infamous for clogging shelves as the series wore on. That said, he at least had fans for his subplot with Scorponok actually going somewhere, which, for this show, is a lot.
Sequelitis: Compared to Armada, which started slowly but improved dramatically in the second half, this show started with potential and utterly failed to use it.
They Just Didn't Care: The series started reasonably well in spite of the bad dubbing, but subplots regularly not being followed up on, poor CGI, a dub that's considered to be one of the worst in TF history, bad characterisation and a stale story all conspired to make this the go-to Dork Age for the entire franchise.
Starscream is reborn as a confused, and angry spirit/being, up until Megatron gets hold of his mind and makes him loyal. He remains that way without his Noble Demon characteristics that made him famous in Armada. And then the pendulum swings the opposite way entirely in Transformers Cybertron, where he becomes a more traditional, yet VERY competent Starscream.
Let's not forget how close he was to the kids last series, especially Alexis. They're still around this time, but do we get to see him interact with them and a possible subplot emerge from this? Nope.
Demolishor went through a whole arc where he struggled with his allegiance. As Cyclonus and Tidal Wide defect back to their old faction, he tries harder and harder to do the right thing, until, in his penultimate episode, he makes his decision and saves Megatron's life at the cost of his own. He's resurrected in the following episode and is considerably less conflicted and quite a bit stupid, implying Megatron messed with his mind. The arc is never brought up again.
Wing Dagger loses his best friend to Shockblast and then tries to avenge his fallen comrade, performing a Heroic Sacrifice. His quest of vengence is almost never brought up when he is resurrected (he has one revenge battle and captures him in his first appearance as Wing Saber, but nothing is made of it after Shockblast inevitably escapes).
There's some of Unicron in every Transformer. That should really go on to mean something or be important somehow. But this is Energon, so it doesn't.
Kicker wasn't just a Jerk Ass in the beginning: when Kicker developed his energon sensing powers as a child, his father had the bright idea to use Kicker as a living energon detector. For years, he dragged his young, pre-teen son around space, where he had to deal with a few mining accidents that nearly cost him his life. The Autobots saw no problems with putting him to work like this, and so Kicker grew resentful of both them and his father. Rather than have him grow to trust Team Prime in a charactery-developy way, the whole "there's a reason he's this way" thing was just forgotten early on and he spends the rest of the series being rude for no discernible reason. It takes until mid-season for everyone else to similarly forget that they don't like it when he's like this.
Team Ironhide's introduction hinted to an amusing vitriolic relationship over Kicker pushing around their idol, probably the nearest anyone got to calling him out on his treatment of Ironhide. However they never interacted after their first episode, and Team Ironhide were killed off shortly afterwards (though Kicker at least had the decency to lay off Ironhide afterwards).
Rodimus, who led a faction of Cybertronians who said Screw This, I'm Outta Here! to The Forever War and hasn't been seen in millions of years, returns, and he and Optimus are far from on the same page. Rodimus' team proceeds to... fall in line with Optimus' within two episodes and never really add much to the proceedings.
The Decepticons never powerlink throughout the series (one gag even implies they are unable to). Despite showing this ability in the previous series, a series that revolves prominently around powerlinks refuses to look into it, also often making their battles with the Autobots rather one sided due to this heavy advantage.
The Woobie: Demolisher (constantly abused by Megatron and forced into a conflict he wants no part of), Ironhide (constantly abused by Kicker and has most of his friends die), and Wing Dagger (fails to save his best friend and never gets the justice he seeks).