I suggested that during Episode One a whole bunch of rich lobbyists are prompted by Sidious' backing to play out their dream scenarios free from Republican bureaucracy.

In my take Gunray invades Naboo because his planet and the Naboo had fought over the territory many centuries ago and he wants to reclaim the planet to buttress his flagging position back home.

If around the same time half a dozen other prominent galactic powers were tempted to make similar moves in isolation they would be booted out of the Republic but Dooku knows the Sith were really behind it. The line Dooku gives Obi-Wan in AOTC in this scenario becomes true.

At first they don't want to break away from the Republic but as they have all burnt their bridges and as nobody in the council seems to be taking Dooku seriously he leads them in an attempt to build a alternative to the failing Republic and fight the Sith (not realising he is actually helping them).

That way Dooku becomes a more tragic figure.

The Jedi are backing the wrong side politically because the people Dooku is defending have been manipulated into doing politically awful things.

They want to maintain the Republic but they don't realise it's already under control by the Sith.

Palpatine can then use them as evidence of Jedi complicity and label the Rebel Alliance as the Separatists reborn once he transforms the Republic into the Empire.