The thing to realise is, for the Jedi, in the Prequels, it's a rigged game and it's been rigged by Sidious:
- Choose A - You're fucked.
- Choose B - You're fucked.
That's what gets set up in the PT and the story is then how it all plays out. In part it also exploits flaws in the Jedi perception by focusing their attention in one place to stop them looking elsewhere:
To the PT Jedi the pre-eminent form of evil is the dark side. The foremost practitioners of that are the Sith. Thus the Sith are the no. 1 enemy for the Jedi. They are then given a Sith enemy in the form of Dooku, who so occupies them they never consider that there is another, unknown Sith active, instead they perhaps assume Dooku was Maul's master. By the time they realise their error, it's too late.
One of the points I really disagree with in the PT is that the Jedi rely entirely on the Force for guidance, up to and including not drawing on practical reason. The idiot line goes: Jedi do not think, they know (via the Force). Well, that's all fine until someone fucks the service supply of the Force, which is also what happens in the PT. It's not simple idiocy at work though, it's thinking you are beyond error so you don't need to look for it.
The PT gets a lot of flack, but I really like how the Clone Wars operated - to destroy the Jedi on multiple levels and embed the Empire so that by the time its declared the Empire has already existed in all but name