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.
Base Breaker: Mikaela. Some wished she was the main human protagonist, next to Lennox, since she was less whiny, more assertive and just more competent than Sam. On the other hand she doesn't have quite enough of those moments so it still feels like she's just there to show Sam is a heterosexual.
Bumblebee has become this, due to his Movie and Prime incarnations being overpacked in case assortments and, especially in Movie BB's case, having too many just-slightly-different versions of the same toy.
Transformers Rescue Bots is filled with Bumblebee toys, including a large playset. Bumblebee only appears in three episodes as a guest.
A lot of fans are bemoaning the oversaturation of Bumblebee, and wishing Hot Shot would make a comeback.
In fact, the creators of Animated vyed for Hot Shot (in a main role, at least), but since execs wanted 'Bee instead, they had to compromise. And for all his charm, he has a lot of screentime and is intentionally annoying.
Simon Furman has Grimlock, Thunderwing and Bludgeon.
While there are more than a few who complain about how he overuses Big Grim, few seem to have any problem with Furman's take on Thunderwing. And as for Bludgeon? The guy's a friggin' Ensemble Dark Horse, proving that even Creators' Petsdon't have to suck.
And then we have Skids and Mudflap. They got almost as much toys as Bumblebee in ROTF, and had more screentime than any other Autobot. Thing is, it's possible that them flopping and flopping hard led to Bumblebee becoming a Creator's Pet.
Draco in Leather Pants: Oh Primus this is such a problem with the Fan Dumb. Some fans take the Well-Intentioned Extremist interpretation to the next level and act as if the Decepticons are the actual good guys rebelling against the "fascistic" Autobots. This often involves conveniently glossing over the numerous horrible war crimes, abusive behavior, and horrific racism that the Decepticons commit. This is especially bad in series that give the Decepticons a sympathetic/tragic backstory or avert Always Chaotic Evil. This often leads into...
Ron the Death Eater: According to some the Autobots were horrible oppressors who are being overthrown by the "heroic" Decepticons. This view pretty much requires that one believes dictators frequently encourage their slaves to express free will and despise cultural discrimination.
Ear Worm: Transformers... more than meets the eye...
Fanon Dis Continuity: Exactly what it is varies from person to person. The live-action movies are especially popular for this treatment.
Fan Nickname: It isn't uncommon to see "OP" for Optimus Prime, and "Megs" for Megatron.
Friendly Fandoms: Somewhat surprisingly with Doctor Who of all things. It helps that many of the better-regarded writers for the franchise are also Whovians; also of note is that Ensemble Darkhorse Death's Head (originally from the Marvel UK Transformers comics) made the jump from this franchise to the mainstream Marvel Universe via an encounter with The Doctor.
My Real Daddy: Simon Furman, who breathed new life into the comics, established much of the lore and characterizations for the franchise, and has wrote a good majority of Transformers comics.
Periphery Demographic: Transformers has a massive and varied fanbase of people from numerous demographics. Hasbro is quite aware of this; the comics can essentially do the things that the children-focused cartoons can't so that adult fans aren't left out.
Rooting for the Empire: A small contingent of fans feel that the Decepticons are the real good guys, and that the Autobots are evil. Granted, a few continuities show that the Bots aren't perfect paragons of justice, and the Cons had good reasons to rebel, but stories where Decepticons take small children hostage (or killa puppy) show that they are NOT nice mechs.
Given a bit more weight in Transformers Animated in which the Autobots are the ruling empire led by someone who's just a bit too willing to do bad things to achieve victory for comfort while the Decepticons are the scrappy rebels, albeit vicious and ruthless ones.
In the IDW comics the Autobot government was evil (well corrupt at least) and the Decepticons were laid off blue collar workers living in slums until this one miner showed up... (Most of the story is set millions of years later, by which point they're rather less sympathetic.)
One of the movie prequel comics showed one part of the falling out between the Autobots and Decepticons was Prime wouldn't allow Megatron to attack a hostile force on their way to Cybertron, until they arrived and started attacking. Megatron was just trying to protect Cybertron.
In the Transformers: War for Cybertron continuity, Megatron was initially a gladiator who rebelled against an oppressive, caste-based society ruled by the Autobots, so initially it was the Autobots themselves who were the Empire and you should have rooted against. But Megatron became too prideful and ruthless, to the point his ideal of a caste-less society was buried by his desire to rule. Transformers seems to have been moving over the years from "Decepticons evil, Autobots good" to an almost Star Wars-like setup, where Cybertronian society badly needed shaking up but the Cons went too far and the necessities of war turned the Autobots into the casteless society the Decepticons wanted, while the Decepticons became too obsessed to remember their original intentions.
Bumblebee is starting to develop into this, due to becoming a Creator's Pet. His less than flattering portrayal in Robots In Disguise under John Barber's pen isn't exactly helping this.
Villain Decay: Usually dealt with by upgrading the villains to new forms (with new toys, naturally).
Animated tried to prevent this by way of making appearances of the Decepticons in season one and most of season two rare, with human villains picking up the slack. This backfired horribly, turning off many fans who wanted to see the Decepticons and didn't want to suffer through countless episodes of the Autobots fighting lame archer and princess-themed villains.
However, as many fans think that the Decepticons' rare appearances, and the sheer effort it took to fight them, successfully kept them from succumbing to villain decay.
Eventually it did kick in, though not severely as some other examples (Well, except for Lugnut).
Hasbro actually tried a line of big, expensive toys for the adult collector, and it didn't sell well enough to keep it going for too long. Turns out the adult collectors are a smaller pieceof the pie than they thought, and kids are in fact the primary consumers of toys. Who knew?
It should be noted just how much of Simon Furman's work fits into this category. When the writer of the bloodbath the Marvel Generation 2 comics became calls something too dark, you know you've taken Darker and EdgierUp to Eleven.
Furman was specifically concerned about the "For Kids" part of this trope. He was very much about darker, more fatal Transformer stories, but he was explicitly writing with an older audience in mind than the cartoon series are marketed towards.
It's a bit understandable, though, if you look at the premise devoid of context: Two factions of a race of alien war machines come to Earth, their war having gone on so long that battling for the resources our planet can give them to continue the war effort is more important than the war itself. The weakest of them has enough power to slaughter dozens of human soldiers and come away with nothing more than a badly-scratched paint job. At best, their feelings towards us are paternalistic, and they look down with a combination of pity and admiration on those of our species who see it as their sworn duty to defend us from them. At worst, they find us repulsive and enjoy slaughtering us when they have a chance. A sunny kids' show is not what you'd imagine it would look like.
Kiss Players is infamous for how ungodly not kid friendly it is. T Fwiki sums it up well: "Although not featuring any explicit nudity or sexual content, the comic consists of a virtually unhalting stream of images clearly designed to evoke various violent sexual situations, from the endless streams of viscous, white liquid that frequently splatter over the scantily-clad-to-nude cast members, to cowering, flush-faced, teary-eyed girls pressed against walls with their hips raised into the air, to the most (in)famous of all, the distinctive image of the Legion's blatant penis-tongue, leaking goo from a goddamn urethra. Putting the cherry on this sundae of depravity, the manga employs an art style that uses proportions specifically and deliberately designed to make the vast majority of its female characters appear as though they are underage (despite the fiction identifying them as being at least old enough to drive). Subsequent translations of the radio dramas also revealed that the show's dialogue was loaded with sexual double-entendres, ranging from humor-based (Optimus Prime deriving pleasure from Marissa rubbing the rim of his gas tank) to grotesque examples blatantly evocative of rape (a shrunken Autorooper forces its way into Atari's mouth and makes her swallow it, followed by her begging it not to "move too roughly inside" her)".