Author's Saving Throw: A Clip Show was made after the show concluded that explained pretty much most of plot holes, like explaining where Devil Z got the Godmasters or why Ginrai looks exactly like Optimus.
Fanon: Overlord being a Duocon is something that never came up in the series but many fans jumped on the idea. Overlord had two different alt modes that combined together for a vehicle mode (A jet and tank just like Flywheels) even though his gimmick was a being Godmaster and Duocons had their own instant transforming gimmick. Decades later this would become Ascended Fanon and Overlord was retroactively called a Duocon.
Germans Love David Hasselhoff: Transformers fans seem to have the liking of the Godmasters God Ginrai and Overlord. The former because his transector looks like Optimus Prime, and his toy is often imported, not to mention having an American reissue (although as Optimus Prime). Overlord is also one of the popular villains, with his toy also imported by fans since his appearance in the anime.
The emotional scene of Shuta putting the baby ahead of fighting the Decepticons. Given he had just lost his father, this is very powerful.
Ginrai telling Sixknight he is a human which causes the latter to ultimately decide the Autobots are better than the Decepticons.
Minerva's kindness towards Cancer, which causes him to question his faction several times.
The Decepticon Headmaster Juniors protesting against the kidnapping of children, and its only when the Pretenders become aggressive that they comply. Given that Wilder and Bullhorn were previously shown as jerks, this lets the audience to the fact that there is good in them.
Mega's care towards Cancer, treating him as her own son. When Cancer is buried under rubble, it is implied that Mega takes control of Overlord and forces him to stand down.
Its an equally heartwarming moment for Giga as it is shown both of them can usually control Overlord, since he is a multi component Transformer. He allowed his wife to stop fighting, even though he lost as a result of that decision.
Overlord trying to persuade Devil Z not to abandon Wilder and Bullhorn, showing that although Overlord can be vicious and brutal, he isint evil to the core.
Moral Event Horizon: Devil Z crossed the line when he ordered the Death Para Machine to destroy the Earth's stratosphere and thus destroy humanity.
If he didn't cross it then, he most certainly did it when he started killing his own soldiers when they said he was going crazy.
Hydra and Buster hace a number of points where they crossed the line.
The first one, and arguably the most debatable one is when they attack Ginrai's friends. Granted, they did not target them intentionally, and they were killed in a case of mistaken identity, but the fact they didn't bat an eye over that is really cold.
The second one is where they kidnap Lightfoot's father and use him as a hostage, giving Lightfoot the choice of either joining the Decepticons, getting his arms cut off, or having his father murdered.
The third one, and the one that is almost certainly a no brainer is when they personally ask Devil Z to remove them from their humanity, seeing it as a weakness.