Creator Breakdown: Bob Budiansky (see above) suffered from stress due to trying to constantly shove in new toys, which led to him leaving the comic. He has since said that he has no intention of working on Transformers again, though that doesn't mean he wouldn't say "no" if Hasbro asked him. His only post-Marvel Transformers work was IDW's faithful adaptation of the animated movie, which was less stress-inducing for obvious reasons.
Executive Meddling: The reason female Transformers didn't appear from the very start. Budiansky was ready, willing and able (Ratchet was even a candidate for an early female character), but the Hasbro execs thought there shouldn't be girls among "toys for boys" in a comic book "for boys". (Human female characters were obviously exempt from this reasoning).
Sequel Gap: After 21 years the comic is finally getting a proper, epic conclusion with Regeneration One.
ShinjiAramaki also did several character designsnote Soundwave, his Cassettes and Reflector, to be specific. and created Perceptor.
Two that pertain to the movie: Several of the film's key animators were, at the time of production, employees of Bebow, Madhouse and Sunrise. Whereas Unicron was originally designed by Hiroyuki Hataike, who would go on to create Outlaw Star.
Jossed: Fanon assumed that the character Dion from the episode "War Dawn" survived the attack on storage yard 67 and was rebuilt into someone important (Ultra Magnus being the most popular choice), seeing as his best friend, Orion Pax was rebuilt as Optimus Prime. In 2010, Hasbro flat out stated that Dion was never rebuilt into anybody else and had not even survived. Also, The Transformers: Wings of Honor continuity had Dion survive the attack, but he was still called Dion.
The Other Darrin: Voice director Wally Burr substituted as Thundercracker for John Stephenson in "War Dawn", and as Ratchet for Don Messick in "Masquerade".
After the death of Roger C. Carmel, Jack Angel took over as Cyclonus.
The Other Marty: Ted Schwartz was originally intended to be Judd Nelson's replacement as Rodimus Prime's voice after Transformers: The Movie, and he still has a few lines (in the recap of part 2 and one line in part 3) that weren't dubbed over by Dick Gauthier in "Five Faces of Darkness".
Recycled Script: "Microbots" has a similar scene to the TMNT episode "Shreddered and Splintered". Both episodes were written by David Wise.
In "War Dawn," Ariel was supposed to die along with Dion. However, members of production realized that since she was Orion Pax's Love Interest, she could simply be rebuilt as Elita One. (This, by the way, is why fans propose Dion was also rebuilt into someone Optimus would know.)
Octane's role in "Starscream's Ghost" was originally intended for Blitzwing, who was banished from the Decepticons in the "Five Faces of Darkness" five-parter. Blitzwing was replaced by Octane to promote Octane's newer toy.