Why did Rodimus so easily accept Optimus reclaiming the Matrix? Because in the previous episode we saw that he was struggling with the weight of the Matrix, he happily embraced the loss of the Matrix and only took it back because he had no other choice. The fact that the one he always knew was the worthier warrior was back was a welcome relief for him.
In "More than Meets the Eye, Part 2", Starscream ends up seriously inconveniencing the Decepticons because he felt the need to test some Energon cubes. This may seem like a boneheaded move, but remember: Starscream used to be a scientist. Of course he'd want to test the Energon to make sure Earth's resources can be safely refined!
Why is Ironhide red? Iron is known to be red in its natural state.
In "The Rebirth, Part 3", the Combaticons are seen building the giant engines on Cybertron. Normally you'd expect the Constructicons to do this, but by this time, their toys had been discontinued, so it made no sense to shill them when the Combaticons were still available.
Why would Predaking be much smarter than the other combiners if the writers ever bothered to read the characterizations? Because his components' altmodes are animals. Whereas the other combiners are amalgamations of minds that don't always get along (and sometimes outright hate each other), Predaking is a pack. When the hunt is on, internal conflicts get put aside.
Sky Lynx's near-insufferable sense of superiority makes a lot of sense when you step back and take a look at his combined non-alternate mode: He's a dragon. How often in modern fiction do you see sentient dragons without an ego?
Megatron's alt mode is a gun, which has to be held by others in order to be fired. A case of What Kind of Lame Power Is Heart, Anyway?? Nope - a gun has only one purpose, and that's to kill people. He chose it in order to be more intimidating!
Why does Megatron allow himself to be wielded in gun mode by Starscream, whom he hates and distrusts? Because when he's the weapon in Starscream's hand, Megatron becomes the only thing Starscream CAN'T shoot.
As this video touches on, there's a lot of Fridge Brilliance tucked into Megatron's alt mode. First, his shots seem more powerful when transformed, providing an incentive for him to transform to be shot instead of shooting himself with his massive Arm Cannon. It also might make sense that this is the case: depending on how Transformer mass-shifting works, the energy of his Fusion Cannon might be "compressed" in his smaller gun mode, making the blasts more focused... essentially making his gun mode shots an Armor-Piercing Attack. Second, he's actually demonstrating a commendable leadership quality, trusting his subordinates to do the job he's assigned them, literally placing himself in their hands to see it done. Third, sometimes his ability to communicate is all mode is diminished or absent, meaning he's essentially turning tactical command of the battle over to another Decepticon, again showing trust but also that Megatron might realize his limitations — a tactical thinker he is assuredly not. Finally, he didn't actually choose that alt form, it was foisted on him by Teletraan-1. The Decepticons seem to have no means of reconfiguring their alt modes, so Megatron is stuck with it and doing the best he can with what he's got.
A combination of Brilliance and Horror: it's established that the Autobots and Decepticons were originally created for to be labor drones and combat droids respectively. The horror comes from the fact that this basically means that the only reason the Decepticons fight is because they’re subconsciously acting out their programming and all the talk about power, glory and destiny are just rationalizations. The brilliance comes from the fact that this means that the reason the Autobots always win in the end is because they Grew Beyond Their Programming and took up the sword.
During "The Key to Vector Sigma" the military thinks the Stunticons are the Autobots. Sounds stupid with Decepticons like the Constructicons and the Triple Changers, until you realize that up until this episode the Decepticons had no normal ground vehicles as transformers. As this was cars and a big rig, that means it practically has the Autobots written all over it.
Even better, as later episode "Masquerade" points out, the Stunticons are made up of a formula one car, a lamborghini, a porsche, a ferrari, and a cabover truck; all vehicles previously seen as the alt modes of prominent Autobots.
In the Season 1 Episode, "Heavy Metal War", Megatron challenges Optimus Prime to single combat, with the loser being required to exile themselves and their army to deep space, forever. Then he cheats, borrowing the powers of all the Decepticons, and to try to ensure his cheating isn't discovered, he orders the Constructicons to destroy Teletraan 1, the Autobots' computer, which would totally narc on him (and it did). Megatron didn't have to kill Optimus Prime in this duel, only defeat him. But what this essentially means is, if all had gone according to plan, Megatron would be "rid" of the Autobots without having to destroy any of them, including Optimus Prime. This puts the cheating itself in a whole new light, as it would have effectively ended the War, but without any more killing of Autobots.
Brawn, Bumblebee, Cliffjumper, Gears, Huffer, and Windcharger are shorter than the others because their toys are carded, making them about half the size of a boxed figure.
Unlike later combiners, the Constructicon team leader forms a leg instead of the torso (particularly the part with the head). This matches the team's characterizations; the Constructicon leader is Scrapper, who despite some of his less noble traits is actually a fairly humble and modest worker who shrugs off any given praise. As such, he just sees being Devastator's leg as part of his assignment. Hook, on the other hand, is a perfectionistic glory hound who craves attention and praise from others, so being the literal head of Devastator is what he sees as the peak of status in the team hierarchy.
The Hate Plague episodes: It's established that the plague went beyond earth to other planets, to the point that the entire galaxy was threatened. Imagine the kind of destruction unleashed on earth occurring everywhere else in the galaxy. That's a death toll measuring so high that there might not be a number large enough to catalog the amount of lives lost. That scene of the two humans apologizing for weaponizing the plague is likely very their last action on earth before they're imprisoned some where in space or executed.
In "Ghost In The Machine", Unicron wanted Starscream to connect him to Cybertron so he could reformat it into his new body. Knowing what we know now about the TF mythos, especially the fact that Cybertron essentially IS Primus in physical form... just what WOULD have happened if that had occurred?
Megatron's altmode makes him extremely vulnerable. Starscream could just crush him under his foot or in his hand. Even if Megatron remains his toughness in his altmode, he could be easily imprisoned while transformed. On the other hand, this is Starscream we're talking about.
What would stop the other Decepticons (especially loyalists such as Soundwave) from simply freeing Megatron if Starscream did imprison him? Also, Megatron mostly transforms into his gun form in battle with the Autobots. Starscream isn't going to attempt to off Megatron while they are being attacked by the Autobots, he is not dumb enough to think it would be a good idea.
touches on, there's a lot of Fridge Brilliance tucked into Megatron's alt mode. First, his shots seem more powerful when transformed, providing an incentive for him to transform to be shot instead of shooting himself with his massive Arm Cannon. It also might make sense that this is the case: depending on how Transformer mass-shifting works, the energy of his Fusion Cannon might be "compressed" in his smaller gun mode, making the blasts more focused... essentially making his gun mode shots an Armor-Piercing Attack. Second, he's actually demonstrating a commendable leadership quality, trusting his subordinates to do the job he's assigned them, literally placing himself in their hands to see it done. Third, sometimes his ability to communicate is all mode is diminished or absent, meaning he's essentially turning tactical command of the battle over to another Decepticon, again showing trust but also that Megatron might realize his limitations — a tactical thinker he is assuredly not. Finally, he didn't actually choose that alt form, it was foisted on him by Teletraan-1. The Decepticons seem to have no means of reconfiguring their alt modes, so Megatron is stuck with it and doing the best he can with what he's got.