Missing Episode: "Return, Our Scorponok!" was never translated or broadcast in America. This changes the audience perception of Scorponok entirely, as it is revealed that he is not actually Alpha Q's servant from before the planet's destruction, but a Decepticon with Fake Memories. The real Scorponok died when Planet Q exploded.
The loss of an episode that both explained a lot of things and was a major turning point in the series rendered a lot of events meaningless or confusing. No one's sure why it was left out.
Old Shame: For many of the actors, but Brad Swaile (the voice for Kicker) in particular.
What Could Have Been: From various sources, it seems there was an awful lot of ideas Hasbro and / or Takara had for the show that never got implemented. Some of the ideas did end up used in the comics, while some didn't.
The Omnicons were originally thought up as evolved Mini-Cons.
Snow Cat, Roadblock, Mirage and Demolishor's dump truck form were intended to be all-new characters by Hasbro. It's pretty likely that Demolishor was supposed to be a new version of Long Haul. This was also the case with a number of redecoes and retools over the line's course, most notably changing Roadblock (intended as a new character and an homage to G1 Grapple) into an upgrade for Inferno - Roadblock's toy bio even still refers to him as if he were a new character.
Alpha Q (snerk) was meant to be Unicron's servant.
Meanwhile, the show writers' idea for Alpha Q was that he would turn out to be a little girl, the princess of Planet Q.