One more comment about the Jedi in this timeframe, which I sort of hinted at here:

The Jedi, previous to this, are not an official "group" but more like samurai who are out doing their own thing... The war causes them to organize- which makes it easier for their enemies to take them out.

Most people are a little suspicious of the Jedi at this point in time. The back to back Clone Wars are blamed on the Jedi. Not because of anything specific they did... but more for not stopping them in the first place. The Jedi are supposed to help keep the peace- the wars have been anything buy peace. A lot of people look to the Jedi to throw off their non-agressive ways and forecefully bring peace to the galaxy. The fact that they haven't means that a lot of people have lost hope and trust in the Jedi. Less devout Jedi have begun to leave the order and stopped self identifying as such to avoid the persecution.

When the masterminds of this second (and last) Clone War are revealed to be Dark Jedi, then the Jedi organize to fight back. Because the Dark Jedi are their responsibility, and because they are besmirching their good name, they rally to defeat them. People get behind them then. And they are rock stars for a season... then the Dark Times begin...