There is a theme present in both Ep1, Ep2, and EU books during this timeline that show us that the Jedi started to loose the Clone Wars after their very first victory. Yoda has the wisest of the comments to Obi-wan and Mace at the end of Ep2 when he says this was not a victory, the shroud of the dark side has fallen. Previous to that in Ep2, Mace makes the comment that the Jedi are peacekeepers, and not soldiers. As early back as Ep1, Qui-gon makes the same comment to Padme that he can only protect her, he can't fight a war for her.

In the book Shatterpoint, Depa Billaba - Mace Windu's former Padawan - goes to Mace's homeworld to help his jungle-tribe of force sensitive warriors fight against the separatist-allied city dwellers. The result is that Depa is slowely eroded by the acts of war. The killing, manipulation, spread of hatred for recruitment, etc all goes against the Jedi code. By the time Mace shows up to find her, he discovers this truth from himself.

By ROTS, the Jedi point of view has been skewed so far from the shroud of darkness that surrounds everything. They have fallen victim to Sidious' trickery to focus on winning the war. The more they focus on this, the more power over the situation Sidious has. This climaxes with the espionage task that the Jedi Council gives Anakin. Ironically, Anakin reminds us how this is betraying his teaching, his friend, and his trust.

Gotta wonder how it would have turned out if the Jedi stayed true to their code and refused to enter the world as anything more than peacekeepers and distant consultants.