Old Shame: Reportedly, Leonard Nimoy was so embarrassed by his participation that he avoided talking about it. Nowadays, it's remembered as one of his better (and few) villain roles, even by Nimoy himself, who was quoted around the time of Revenge of the Fallen as wanting very much to be a part of Transformers again. The opportunity finally arose with Dark of the Moon, wherein he plays Sentinel Prime.
When Megatron got upgraded to Galvatron, his voice changed to Leonard Nimoy during the story itself. After the movie, he changed back to Frank Welker, but now with his balls being squeezed uncomfortably.
In the series, Ultra Magnus went from Robert Stack to Jack Angel, Kup went from Lionel Stander to John Stephenson, Tony Pope replaced Eric Idle as Wreck-Gar, Roger C. Carmel took Orson Welles' position as Unicron's voice actor, and Rodimus Prime's Judd Nelson became Richard Gautier. John Moschitta stayed on board, however.
There is a long-prevailing myth among the fandom that Orson Welles died before the recording of Unicron's final lines and that Leonard Nimoy completed for them - with the recordings speeded down to match Welles' pitch. Voice director Wally Burr has since debunked this in interviews, however.
What Could Have Been: Originally, they were to kill Smokescreen instead of Wheeljack, and Red Alert, Trailbreaker, and possibly Mirage would bite the dust as well. Ultra Magnus, Red Alert, Sideswipe, and Tracks would get a scene where they fight Devastator, leading to Red Alert's death.
Shockwave was to die by (literally) Unicron's hand when he comes to Cybertron, thus explaining his absence in season 3
Likewise, the earlier drafts of the films featured many, many different elements, in one revision, Windcharger was to be flown up and torn apart by Cyclonus, his remains falling down on a shocked Blaster. Another version described Ironhide and Ratchet's deaths as them being fused together from all the laser blasts, then blown apart.
At one point, Megatron was not to be jettisonned from Astrotrain, but brought back to Cybertron and killed by a falling statue while other Decepticons fought for leadership, with his ghost ("life spark"), as well as ghosts of Decepticon legends enshrined nearby, being gathered by Unicron to become Galvatron and his troops.
Just before facing Megatron, Optimus Prime is inexplicably missing his rifle. The reason for this is a cut scene, where Blitzwing was supposed to knock it out of Prime's hands, before being hurled away by Prime.
Early drafts included a large number of generic Decepticons participating in the assault on Autobot City. That way, Perceptor's comment about the Autobots being outnumbered would have actually made sense.
The revelation of the Quintessons being the creators of the Transformers originated in an early draft.
Also, Optimus merges with Cybertron, transforming into a giant planet-sized robot to fight Unicron.
In the original art and storyboards, the Junkion's homeworld was intended to be a spherical planet, with several rounded slabs seeming to rise off of its surface. In the end, only the "northernmost" rounded section of the planetoid was retained on film.
Story editor Flint Dille disliked the original script so much that he hastily wrote another one, titled The Secret of Cybertron, featuring Optimus journeying to find the Transformers' origins. This is where the idea of a transforming Cybertron originated from. Also, Unicron would have been a pawn of the Quintessons. The execs however quickly dismissed the script.
At one point, the writers toyed with the idea of having Unicron threaten Earth as well as Cybertron.
Magnus would have been simply pulled apart during his "death" on the Planet of Junk. The animation even shows the Sweeps firing laser "ropes" at him. However this method was deemed too gruesome, so in the finished movie, the "ropes" suddenly turn into regular laser blasts, and Magnus just explodes. The part where the Junkions put him back together is also a remnant of the original scene.
Some of the original script drafts didn't feature the Matrix — Unicron would have simply torn himself apart. When a similar concept to the Matrix was introduced, it wasn't the artifact we know it as today, but was for a while imagined as the ghost of Optimus Prime transferring into the body of Ultra Magnus. The toy of Ultra Magnus was basically just a white Optimus wearing super-armor, which is where the idea came from. Since the "ghost" never appears in the finished movie, Magnus's unarmored form was never featured in the series. Some later incarnations of the character did however present him as a white and blue-colored version of Optimus Prime.
Unicron's working name was "Entity". In one early script, Unicron was only the name of his planet mode, with his robot form being called "Ingestor". The Reveal at the end of the movie would have been that Ingestor is actually the planet.
In another early draft, the characters who would later become the Predacons in the cartoon's third season would have starred as Autobots, called Anibots. The would have combined into a dragon, rather than a humanoid giant.