Let's start from TPM and go on: what the hell is Palpatine (Sidious) trying to do with Nute Gunray? Why is this war going on? Why does Dooku inform Obi-wan of Palpatine's evilness, but still work along side Palpatine? Why did everyone suddenly realize that Palpatine is bad right at the end? How does this all connect?
This is just my interpretation but I think that Palpatine is trying take control over the galactic government by turning it's mechanisms and necessary bureaucracy against itself.
The Republic is a galaxy spanning organisation and works by demarcating it's authority into spheres of interest.
You have the senate, the courts, the commerce guilds, the military and the Jedi (which act as dual cleric/martial clique).
Under the guise of a politician with influence Palpatine is almost to the top of the senate. He needs a little boost to get him onto the Chancellor's podium so he encourages a section of one of the commerce lobbies to invade Palpatine's own territory. This creates sympathy for himself in the senate and distrust of the entire commerce field (people don't trust the bankers).
This sympathy translates to elevating himself to control over the courts which almost allowed the invasion to become entrenched because of it's sluggish procedures.
The Trade Federation and it's other commerce pals are isolated and form a separatist movement claiming they were lead astray by corrupt politicians (people don't trust politicians) and they create a mechanical military force to defend their independence from the Republic. Their leader is a strategically placed former-Jedi.
Dooku has become a Sith Lord like Palpatine and desires to corrupt Obi-Wan into becoming his apprentice so they defeat Palpatine together and replace him.
Palpatine is aware of this and desires to corrupt Anakin into becoming his apprentice so they can defeat Dooku together and Anakin can be his replacement.
Palpatine uses the Separatist militarisation as excuse to expand the Republic's own military force and an arms race ensues resulting in a Galactic war which the Jedi will be called to defend the Republic.
Either camp could lose and Palpatine/Sidious would win and claim the Jedi were the invisible hand behind the war.
By manipulating all the factions, that could detect and defeat his plans, to fight each other instead of noticing what he is doing (until it's too late) Palpatine gets the Republic to dismantle itself.
He then rebuilds it as his own private Empire. The tangle of bureaucracy of the Republic is replaced by a clique of competing regional governors keen to show loyalty as to not lose their position and lives.
This makes it all sound much more interesting than it actually turned out to be.
It's hard enough to do IClaudius in the context of a series of family adventure yarns but especially so when you throw in goofy cartoon nonsense, fart jokes and awkward romance scenarios.
What makes it such a muddle is Lucas doesn't build both factions as being sufficiently righteous or even self righteous enough to command loyalty.
The Jedi are a bizarre bunch and difficult to sympathise with and the seperatists are cartoonish bad guys. The robot and clone armies are faceless and dehumanised to the point where it's difficult to be emotionally engaged in their battles beyond the spectacle. And normal people, people we might have some point of connection to, are practically nowhere to be seen.