The concept of the multiverse
The concept of the multiverse back in 2004 was'nt as advanced as it is today. Yet it had made huge steps,which were more than enough for a project centered around this concept to enter production. Instead of Transformers Energon,Transformers Armada's sequel was supposed to be Transformers SuperCross,a 4 seasons show centered around transformers from across the multiverse,teaming up to defeat Unicron. Back then,Unicron has been described as a multiversal singularity,travelling between universe at will and so,this idea was the centered of the show,as even characters from G1 were trapped within Unicron.
Season 1
Picking up after Armada,everyone is trapped within Unicron alongside other transformers from other universes and they learn of Unicron's goal to erase all life and all existence. Everyone,both Armada and G1 characters team up to get out of Unicron and stop him. Unicron's power influenced everyone,bringing both new powers and some issues,such as the minicons becoming omnicons and Megatron,who believed he can control Unicron if he touches his spark,was mutated and went insane. Unicron is searching of allsparks,which are the most pure sparks. (Kinda like what they did in Transformers Animated.)
Season 2
The Autobots and the Decepticons returns to Earth 4 years after Armada to continue their battle. The kids from Armada are back. They did this to trick Unicron into travelling to the other side of the universe. Megatron begins to get even more sick from Unicron's influence and being mutated further,thus he is replaced as leader of the Decepticons by someone else. In the coming battle against Unicron,the Autobots and the Decepticons seek to recruits allsparks to aid them,thus characters from G1 and Beast Wars are found and recruited. The power from Energon ae featured here as well. A precursor of them,at least, (The combination thing)and the Decepticons also gets war-like powers which fits their personalities. Everyone eventually decides to go to Cybertron to stop Unicron and prevent him from attacking Earth.
Season 3
Unicron intercepts them and is in pursuit of them across the universe. But with their powers,they can hold him off a few times. The Ark is also attacked by the Decepticons as they wanted to get to Cybertron first. Megatron regains control of himself and gets a new form,which allows him to retake command of the Decepticons and Unicron destroys the universes of other transformers,thus keeping them trapped in the Armada universe forever.
Season 4
Both sides build massive armies on Cybertron to kill Unicron and are aided by Primus and Vector Sigma. The ghosts of several classic characters join the fight and in the end,Unicron is killed but his spark is set adrift in space,leaving a door open for his return in the final part of the trilogy. Those ghosts return to Primus to be reformatted. Cybertron is restored but the Decepticons decide to leave,but they wish to return to Cybetron one day to continue the war.
The cut characters revived through Cyberverse
Characters such as Cheetor,Rattrap,Soundwave and Grimlock,among others were meant to be part of the action. Cyberverse did revive a bit of this concept but SuperCross seems to have been a highly ambitious project in its own right.
Cancellation
The reason behind this show's cancellation is a complete mystery,as well as the fact that Hasbro has made the choice to actually go on with a different project (Energon) and committed a big mistake for the franchise rather than following a more ambitious and better fleshed out project to see the light of day. However,it is believed that the idea of including several characters from other continuities along with the Armada one might have required some more budget in order to have it put together and executed.
Cyberverse
The idea of the multiverse was'nt forgotten,as it was at least visited in Cyberverse. I'm not counting the Transtech comics and the Robots in disguise and G1 crossover (Portal).