I also wonder, forgetting about the existing cartoons entirely, could another story be told with the same gimmicks and cast that makes the whole trilogy more cohesive and interesting?
I mean, that's kinda what I was doing in my head-verse as I was watching it (and I assume others were as well).
No time to dig out my old notes right now, but from what I recall:
(Note: I was specifically looking at this as a follow-up to my sorta-G1/BW)
ARMADA:
The Minicons appear out of nowhere as the Great War is winding down (eventually revealed to be a suicide-plot by the now-extinct Quintessons), leading to a pair of Autobot and Decepticon strike teams descending on Earth. The action crescendos in a showdown in Unicron's severed head, where the Quintesson-programmed Minicons were intended to reanimate the planet-eater to assimilate Cybertron/Vector Sigma (foiled as in the show by the interference of the human kids, granting the Minis their free will). Unicron's head is teleported away to parts unknown with Megatron still inside it, the Minicons depart to establish an independent nation, and an era of relative peace descends on Cyberton (many Decepticons go rogue and flee to the fringes of society).
ENERGON:
Scientists Signal Flare and Skyfire create the Omnicon program (intended to allow normal Transformers to handle and process raw energon without being overloaded). The technology is stolen by Scorponok and his pirate crew, forcing Signal Flare, Skyfire, Arcee, and Roadbuster to undergo the process to stop their rampage. Meanwhile, the last living Quintesson is brought out of stasis by the barely-functional Unicron. Upon learning about his peoples' extinction, Alpha-Q reanimates Megatron (who then recruits Scorponok and enslaves Starscream) and embarks on a plan to destroy Cybertron once and for all. Unicron is reanimated, betrays Alpha-Q (Starscream gains his free will back), is defeated by the Omnicons/Terrorcons --and collapses into a subspace singularity that threatens to consume the entire Cybertron system!
CYBERTRON:
As Cybertronian refugees scatter, Vector Prime (less Gandalf and more Uncle Iroh, who eventually adopts Starscream as his Zuko) arrives and sets the Autobots searching for the four
other Matrices (which even Optimus didn't know about). Meanwhile, Wheeljack introduces his newest invention: Force Chips, built with Omnicon energon-manipulating technology, and able to serve as a sort of single-use Minicon (granting the same kind of power-up, but only until the chip burns out and has to be replaced). The final battle defeats Galvatron once and for all, collapses the singularity, and results in the creation of a new planet: a primordial world inhabited by tentacled beings similar to those that first evolved into the Quintessons. Given a new chance at existence, in the distant future they will become the Vok. . .