Actor Allusion: In "The Agenda: Part Three", Silverbolt looks up at Venus in the sky and says it reminds him of Blackarachnia. Blackarachnia's voice actress is Venus Terzo.
Ascended Fanon: The Predacon base's name, "Darksyde", came from a fanonmisinterpretation of a line spoken by Terrorsaur in the episode "Equal Measures". ("Welcome to the dark side!") It was given an official name first in the Beast Wars Transmetals video, and then in the prequel video Dawn of Future's Past.
Deleted Scene: The final episode had a short deleted scene where they put the original Megatron's spark back into his body, resolving what seems like a pretty big oversight in the final cut.
Fake Russian: For whatever reason, Ravage was given a Russian accent.
Promoted Fanboy: Benson Yee, operator of the popular web site bwtf.com and convention visitor. He was approached for G1 knowledge and received a 'consultant' credit in certain episodes. There's a lesser version of this where several fans get minor mentions in-series (usually in the names of sectors on the map and such).
In the episode "Dark Designs", Waspinator receives what seems like brain damage, and is called wacko. He responds by calling himself Wonko The Sane, the name of a moderator from a G1 fan chat room.
Serendipity Writes the Plot: The reason why there are so few characters compared to G1 is because CGI was quite expensive when it was created, forcing the creators to limit the number of characters on each side. Of course, fewer characters meant a stronger focus on the characterization of the existing characters, so it wasn't all bad.
Technology Marches On: The Maximals are several times seen using data discs that strongly resemble floppies.
Towards the end of "Dark Designs," when Cheetor asks Rhinox what it was like to be a Predacon, he answers "it's like you're three gigabytes of attitude on a two-gig hard drive." No, he didn't say flash drive, he said hard drive.
Waspinator was going to be sacrificed at the beginning of the second season, but his popularity as The Chew Toy saved him, with Terrorsaur being sacrificed instead. Scorponok was already planned to die, however, because Inferno was a more entertaining character and would serve as The Dragon to Megatron even better, giving him little reason to remain alive. Both characters who perished did so because the costly limitations of CGI at the time (which lead to a limited character count) meant that characters needed to be removed so that new ones could be introduced and promote the toyline, among other things. Incidently, this also lead - in part - to the meticulous plotting of Dinobot's redemptive Story Arc, so some good came out of it all by the end.
Waspinator and Rhinox had Transmetal toys in the toy line, even though they never changed bodies in the show. This becomes an important point for Rhinox if you support the theory that he decides that Cybertron should be made purely technological in Beast Machines because he had become hateful of his comparatively useless beast mode.
"Dark Glass", a very dark episode since scrapped that would've filled in a nasty little Plot Hole dealing with Dinobot's Evil Knockoff during the series' finale.
For the series finale, Mainframe wanted to have the Maximals fly the Ark and engage the Nemesis. On top of that, the Nemesis would have been manned by revived Decepticons Thrust, Dirge and Ramjet. Budget and time constraints force them to drop the idea.
On top of that, it was originally intended that the two-part Grand Finale was meant to only conclude Season 3 - except as a three-part story, with the preceeding Vok-based episode (that introduced Tigerhawk) being the 1st episode. It would have explained Tarantulas' past and motives in greater detail and revealed the reasons for his hatred of the Vok. When Executive Meddling (the desire to create the controversialBeast Machines) kicked in and resulted in Season 3 being the last season (dropping a potential Season 4), this idea was scrapped and the resolution to the "Tarantulas vs. the Vok" became an Aborted Arc. Remnants of the writers' idea do appear in the Spin-Off comics, however.
In "The Agenda, Part 2", the writers wanted Frank Welker to reprise his role as G1 Megatron. Sadly, M. Welker had a very busy schedule and the cost involved for just a few lines prompted the writers to drop the idea. Gary Chalk filled-in for the role.
In this very same episode, when Ravage transforms in cassette mode, the original Transfomers cartoon theme song was meant to be played. However, copyright issues complicated things so the idea was scrapped.
Speaking of Megatron and Gary Chalk, he originally auditioned for this show's version of Megatron. The role went to David Kaye, however, and he ended up voicing Optimus Primal instead.
Insecticon - one of the first Predacon toys to be released - was originally going to be featured in this series, most likely as part of the original Predacon line-up. This appears to have been learned when Ben Yee's website featured a script draft of "Power Surge" in which Insecticon had dialogue.
"Fallen Comrades" was originally going to introduce Wolfang. Of course, between a certain new toy about to come out, Wolfang's own toy being old news and that tinkering Cheetor's existing character model/design would save time and money, Tigatron was used instead.
Along with Dark Glass, there were two other episodes that never got made.
The first, A Greater Ape, would feature Optimus believing himself to be a real gorilla after a blow to the head. He would later join a gorilla troop and fall in love with a female ape before an attack by the Predacons would jog his memory. It wasn't made due to the number of new models that would have to be made for the episode.
The second, called Bitch Wars, (which was hopefully just a working title) would have Airazor and Blackarachnia leaving their factions, then teaming up and start their own all-female faction. It was not made because the writers had no idea how to deal with the concept realistically.
Rattrap was going to be a more tragic figure. Based on the exposed "brain" on his toy, Rattrap was going to be heavily malformed due to faulty scanning equipment. Over the show, Rattrap would learn to overcome his disabilities and become a competent warrior. It was scrapped because the technology was not yet able to render his organic innards correctly.