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.
Does Tankor/Rhinox willingly choose evil, or is his shell program still operational? Bob Skir says the former is true but the voice actor's performance and visuals point either to the latter or that he's simply gone insane.
Was Megatron just pretending that Savage/Noble was a wild animal driven purely by instinct, or was he really like that and useful?
Better on DVD: The series really does work better as a single narrative rather than as an episodic series.
Complete Monster: Megatron, through the entirety of Beast Machines. 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.
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. Tankor tries to be this, but Megatron seriously out gambits him.
Megatron apparently decided to use this in his tank instead of energon throughout the series. 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.
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.
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.