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.
Tankor. The writers intended him to have chosen evil of his own free will after having been twisted by his time under Megatron's control. A popular fan theory is that he wasn't evil — his actions were caused by input from his awakened spark being filtered through a shell programme. Both interpretations fit what we see on the screen. (Given that, upon his death, he seemed genuinely repentant, the Shell Program makes a lot of sense.)
Was Megatron just pretending that Savage/Noble was a wild animal driven purely by instinct, or was he really like that and useful?
Ass Pull: Though well-received, the reveal that Thrust actually has Waspinator's spark rather than Silverbolt's borders on this.
How the Hate Plague was dealt with. Since the original solution - the Matrix of Leadership - was out of the question, Optimus had to craft an answer that even the Transformers Wiki admits was pulled "out of his monkey butt".
Audience-Alienating Premise: One reason why it was so ill-received when it first came out. The surviving heroes of the Beast Wars now forced underground on their own homeworld, their species subjected to a virtual genocide, and struggling to survive against an overwhelming evil force, all set against a backdrop of things like nature vs. technology.
Better on DVD: The series really does work better as a single narrative rather than as an episodic series.
Complete Monster: Megatron was already a huge bastard in Beast Wars. This show, however, takes it Up to Eleven. Here, he's responsible for the de-sparking of 99.99% of all the Transformers on Cybertron, meaning, effectively, he stole their souls. Then, he tore apart every last one of those vacant bodies and recycled them into his Vehicon drone army. When some of the last Maximals known to exist crashland on what is now his planet, he captures them, gloat over them, and seeks to de-spark them now too. And, finally, he decides to devour/absorb all the sparks he's stolen, becoming God in the process.
Contested Sequel: Between longer story arcs, and a darker tone compared to Beast Wars, fans of the original either think this was a good follow-up, or a joke to the franchise.
Critical Backlash: There were some Beast Wars fans who still enjoyed the show as well as newcomers. Most of the complaints were about the many changes to the characters' personalities and behavior.
All of the Vehicon generals were, to some extent, particularly Jetstorm and Thrust.
Diagnostic Drone was well-liked, enough to appear in other continuities after Beast Machines.
Franchise Original Sin: Inverted! A lot of aspects from this show that people complain about (stronger continuity, darker storytelling, In Name Only characters, etc.) would later be used to good effect by later Transformers series such as the Dreamwave and IDW comics, Transformers Animated, and Transformers Prime. One could consider this show an experimental first step before it's ideas, themes, and methods were perfected by later incarnations of Transformers.
Genius Bonus: The title of the episode "Prometheus Unbound" refers to the Greek legend of Prometheus. Anyone who knows about the myth will get why that is notable. Let's just say that it heavily foreshadows how the series ends.
It Was His Sled: Thrust is actually Waspinator. Even people who haven't seen the series know it.
Jerkass Woobie: Nightscream has pretty solid reasons for being messed up... yet the fan consensus seems to be that his annoying qualities outweighed his sympathetic ones.
Rattrap in "The Weak Component." His making a deal with Megatron is certainly questionable and often a Never Live It Down moment, but considering the way his own teammates (save Optimus) treated him, he had the audience's sympathy.
Magnificent Bastard: Megatron is still the master of this. Tankor tries to be this, but Megatron seriously out gambits him.
Narm: The bizarre designs for the Maximals' robot modes are a little hard to take seriously at times. In particular: Rattrap having a wheeled axle in place of legs, Blackarachnia's Klingon forehead, Nightscream's floppy hair and general plastic-surgery looks, and the way every character's eyes pointed in two different directions on a regular basis.
Megatron apparently runs on this instead of Energon... He started by spreading a deadly virus across the planet, followed that up by building an army out of mecha-corpses, and decided to finish by stealing the souls of his entire species long before the maximals landed. He only got worse from there.
Blackarachnia's faceplate coming up, revealing the extra sets of eyes. Talk about putting your Game Face on.
Scapegoat Creator: Bob Skir received a great deal of criticism from the fandom - to the point where he had to cancel a convention appearance because he was receiving death threats. While he was indeed one of two story editors, he was blamed for everything a given fan had an issue with. Not exactly fair, especially as Skir didn't develop the series himself and was working from what Marv Wolfman started. Notably, Marty Isenberg (the other story editor) never received such vitriol and his being named story editor of a later show was not met with disdain. This all may have been an unfortunate result of Skir making himself available via his website to fans, who incorrectly took him as the ultimate authority of the show.
Shocking Swerve: Thrust being Waspinator instead of Silver Bolt, and Silver Bolt actually being Jetstorm when all of the earlier hints stated that Silver Bolt was Thrust.
Take That, Scrappy!: In "Survivor," Nightscream belittles the rest of the team for losing the Beast Wars. Rattrap responds by knocking him to the floor:
"You watch your mouth, junior! I've lost friends in that war."
For some, Optimus became The Scrappy due to his endless and self-righteously indignant babbling about how "WE NEED TO RESTORE THE BALANCE!" and becoming so fanatical that he was like a Knight Templar. Thus when Cheetor called him out on his plan to obliterate all the mechanical life on Cybertron—which essentially would have made Optimus an eco-terrorist—many fans rejoiced upon hearing Cheetor's speech. Many felt that Optimus had degenerated into a nutjob who was fanatically following the orders of the vague and mysterious Oracle without question, and needed to be snapped out of it.
It helps that the entire point of the first season finale and second season opener seemed to have been about how Optimus was descending into fanaticism and needed to stop himself. He's even brought that delving into that made him Not So Different from Megatron to the point where, a bit in dream sequence, Megatron himself calls him out for it.
Optimus learning what really happened to Rhinox - prompting the big ape to let out a Big "NO!".
They Changed It, Now It Sucks: And how. The changes to several of the character's personalities were a very sore point for fans of Beast Wars, for one.
Vindicated by History: Thanks to the Unicron Trilogy's overall bad reception, this series is often seen in a much better light. It's hardly universal, of course, but still quite a feat considering the backlash it once received.