I personally like the idea of Dooku being ahead of the game.
It would be great to have him inserted into the council meetings in TPM as a hologram (Naboo isn't the only world where trouble is being stirred up and he wants to get to the bottom of it and is more hands on than the rest of the Council).
The council send Dooku's protégé Qui-Gon and his apprentice to investigate the Naboo crisis on their own rather than mounting a full investigation and Dooku is resentful when Qui-Gon ends up paying with his life.
When Gunray and some of the other commerce based groups come to him with evidence of a conspiracy he listens when everybody else just thinks they are covering their backs.
When the council refuses to listen to his theories he goes alone thinking the Republic is too far under the sway of a hidden but powerful menace to be saved from within.
The droid armies are only built to defend the Separatists from a potential attack from the Republic, something he hopes will never happen.
Palpatine uses that as grounds to build his clone army and start the war.
I'd even move the Death Star plan into ROTS as their final desperate attempt to turn the tide on a war they know they are about to lose and have them try to negotiate peace only to have Palpatine send Vader to finalise the deal.
It makes the story more subtle and the conspiracy less Ickian.
Having Jedi on both sides of the war makes it easier for Palpatine to blame it all on them once he has all the power he needs.
It's essentially the same story but made more believable.