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 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!
Why is Ironhide red? Iron is known to be red in its natural state.
Several times, the Ark is said to contain "secrets" that would result in disaster if they ever fell into Decepticon hands. This raises some questions:
If those "secrets" are so potentially devastating, why didn't the Autobots ever use them against the Decepticons?
If the Ark is that important, than why would the Autobots risk it by using it to clear away the asteroid field that threatened Cybertron? They could have achieved the same results with a fleet of smaller, less important ships.
During the Target: 2006 storyline, Unicron is revealed to have ensnared the minds of Hot Rod, Kup and Blurr so they could go back and sabotage Galvatron's plan, calling the process "laughably simple". If that's the case, than why did he even bother sending Galvatron after the Matrix, when he could have just compelled a group of random Autobots to ambush Ultra Magnus and destroy it?
It is eventully revealed that the entire Transformers race were meant to be Primus' ultimate defense against Unicron. If they were meant to battle Unicron, then why did Primus make them so small compared to him? When Unicron finally shows up, he easily crushes many Transformers. If they were supposed to battle Unicron, then making them a mere fraction of his size was an incredibly poor design.
Prior to Unicron's arrival, it is revealed that a group of early Transformers were infected by Unicron's evil, and instructed to lie in wait until Primus announced who would lead his children into battle, and attack him. How did those guys manage to survive the Autobot/Decepticon war? Countless members on both sides were wiped out, yet Unicron's followers somehow managed to survive in enough numbers to give Optimus Prime and Scorponok trouble.
The Decepticons forced the Neutralist scientist Spanner not only to build the Space Bridge, but become a part of it. Many issues later, the Decepticons are shown to have adopted a new, more efficient method of transport. This raises the question of what became of the Space Bridge and Spanner. Was he dismantled, repurposed, or even destroyed (as the Decepticons had no more use for him)?