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.
An implicit explanation is given in Transformers '84; The Ark was a lure for Decepticon High Command, so that they could be taken out by having the Ark crash on a distant world.
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.
They probably remained Neutrals. Its not the safest life (since even Autobots look down on you and don't make an effort to preserve your life), but it does keep you off the battlefield and more importantly, alive.
Several reviewers have said that Fortress Maximus is acting out of character during Time Wars when he orders the Autobots to kill Rodimus, Arcee, Ultra Magnus, Kup, Blurr and Red Alert. However, Fortress Maximus is binary bonded to Spike Witwicky and Optimus Prime, Snarl, Blaster, Hardhead, Brainstorm and Highbrow had explosively vanished and then been replaced by the aforementioned Autobots who say (paraphrased) "Hey, we're from the future!" Wouldn't that make anyone slightly suspicious? Likewise, the reason why Ironhide is the one to say Optimus and the others are dead despite having been present during Target: 2006 where Optimus, Prowl and Ratchet were transported to Limbo. However, the present day Ultra Magnus never told Ironhide or anyone else about the whole mass-displacement issue.
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)?
They actually still use the Space Bridge a few more times after that, such as bringing the Micromasters to Earth. As for Spanner, series writer Bob Budiansky gave his thoughts on that, and reasoned that in the course of the fight between Blaster and Straxus he was so badly damaged that he died, leaving the bridge as an inanimate object.
As TFWiki points out, in The Legacy of Unicron!, Unicron's goal is to use a time portal to retrieve Galvatron from the past. However, given that Galvatron mass-displaced Skids via time travel, would Skids have remained trapped in Limbo forever?
