Show Accuracy/Toy Accuracy: One major downside of the show came with Hasbro testing out making the same character at different price points (so you can have the characters you want without breaking the bank), but used radically different designs for each size class. The characters were designed at the highest price point but the early toys looked nothing like them and did not sell nearly as well (to say nothing of the quality of the line in general). For comparison here is Optimus in Beast◊ and Robot◊ form, and here is the deluxe◊, mega◊ and supreme◊ versions of the toys.
Story editor Bob Skir really wanted Nightscream to be a female transformer, with a design and personality much like Newt from Aliens - he even "argued 'til I was blue that our new bat be female", to no avail. Executive Meddling ensued. As such, the character ended up an Expy of John Connor from Terminator 2. Skir has since stated this probably was not the best idea, even if it gave them a personality to base Nightscream off, because even many fans of T2 found John Connor the worst aspect of the movie (whereas Newt is widely beloved by the Aliens fanbase).
In "Fallout", Dinobot's ghost was meant to serve as Primal's guide in the Matrix and his Spirit Advisor for much of the series.
Transtech, the similarly-scrapped sequel to Beast Machines.
There was originally to be a small section with Obsidian and Strika falling back to Cybertron and refusing an upgrade as self-punishment for their actions while Megatron misled them. It was cut due to time constraints.