alright I'll try to answer somethings as someone that knows the original stuff well
@makingmusic the cube seems to be a modification of the autobot creation matrix which creates transform life and is the essence of primus, the transformers god and creator in the comic,
The creation matrix is not be confused with the autobot matrix of leadership which is effectively a bomb intended to destroy unicron... I guess
the cube seems to have been corrupted by megatron, hence why it creates evil transformers, much as the matrix did in the comic's after prime's death (or should I say one of his many deaths)

@soriku
okay I know who your talking about now, basically bumblebee's substitute for the armada series, I wouldn't mind if they used some newer characters,
which outside of the dreamwave comic I know nothing about as far as story goes

side note Thunderwing or bludgeon introduced as pretenders would be sweet in a sequel as well

people should probably try to pick up any transformers written by simon furman if they want some awesome transformers reading

 actually I didn't take as the decepticon's won but cybertron was  a dead planet, which is why transformers were searching for the cube

as far as bringing back megatron, I'd imagine they'd wait until they're nearing a unicron movie

though if soundwave appears I'm sure he'll be looking for megatron 

I thought that both Matrixes were one and the same? The Autobot creation matrix was Primus' spark after he fused with the Quintesson creation program on Cybertron, forming Vector Sigma. After a few millenia, various transformer religions grew up, one viewing the matrix as a weapon they would use to defeat Unicron.

At least that is what I remember.

@ Superhunk: When Starscream took over the Decepticons in original story, Megatron was thought to have been destroyed, but he turned out to still be alive. It was not the same time as when Megatron was recreated in the form of Galvatron. However, in the movie, Megatron was destroyed, no doubt about it. Does Starscream also take over when Megatron was completey destroyed in the original story as well? I can't remember.

Megatron comming back as Galvatron would be badass.   It would also be fairly true to the cartoons.  Everywhere from G1 up Megatron after suffering a huge defeat would come back as Galvatron.

Soriku, as masschamber said, Hot Shot was really just a Bumblebee replacement.  No point in having both of them.  I don't mind if they add some of the newer characters I guess. 

 THe matrixes are all different transformers universes are numerous, I assume you are talking about the armada/energon cartoon story line.

In the cartoon the transformers were created by the Quintessons created and freed by alpha trion, though everything is rather arbitrary, as it was a saturday morning cartoon,

In the original comic line cybertron is the body of primus embedded in an asteroid used to create cybertron and the transformers to live on in his place after he destroys unicron , now getting into generation 2 transformers, the swarm, and Liege maximo stuff gets really complex, that doesn't even include the awesome uk stuff and death's head, xemerate xaaron and what not

in the original cartoon when Megatron was badly beaten in the movie starscream temporary took over till the reborn galvatron offed him, though screamer would be resurrected by unicron in the 3rd season, I don't know what happens in the Japanese story line, though I do know Galvatron is eventually defeated when the headmasters hold hands and spinning at him, no I am not making that up

The storyline I know seems to be a combination of the armada/energon cartoon and the comic to which you prefer.

Basically, Unicron destroys everything. Primus hides in a giant body of mass that is later formed into Cybertron by the Quintessons. THe QUintessons essentially turn the planet into a giant factory, creating slave bots and gladiator bots. Primus awakes, and begins implanting sparks into these machines forming them into what later became known as Autobots and Decepticons. The Quintessons try to destroy Primus and his "children" so Primus joins himself to the Quintesson creation matrix to form Vector Sigma. Under his guide, A-3 (aka Alpha Trion) defeats the Quintessons.

Then the various struggles between the decepticons and the autobots ensue. Maximo destroys Primon (Primus' physical form and guardian of sorts, taht originally contained the Matrix) and combines himself with the matrix, thus transforming himself into Liege Maximo. The autobots get pissed. War ensues. The autbots become guardians of the matrix. Primus uses "the Guardians" (the converted Quintesson "Dark Guardians" used to defeat the Quintessons) to stop the war between the two factions.  Peace takes hold of the planet, and the various religious sects form, one of which believes that the Matrix is a weapon to be used against Unicron.

Peace breaks down, more wars ensue, Cybertron's resources are depleted. Optimus leaves to find more resources. Megatron pursues. Fast forward a bit and you end up in 1984 on planet Earth.

That's about what I remember. 

ah a see then then I see armada and its lineage attempted to reconcile all story lines into one, they actually did a decent job too,

However I'll I stick with my furmanian transformers

just out of curiosity does anyone actually like that actrocity beast machine? mercy that did a disservice to the magnificent beast wars

Beast Machines was horrible.

Beast Wars, however, kicked serious ass. I had to have seen every episode 3-4 times. It used to come on every morning before school for like 3 years straight, so I saw the series 3-4 times straight through, haha.

For all those interested, I just found this really cool website with a general history of the Transformers Universe:

http://www.angelfire.com/tx3/scorpionsnest/tfhistory2003.html

 nice sit, basically this author attempted to unofficially amalgomize the universes, so that's what your talkings about got it, well done site but I don't think the transformers require a single univers, 

helpful site though for a general over view of alot of information