I also agree with the wiping out of the Jedi Order. I didn't see them as evil, and wiping them all out seemed a bit harsh, but it was almost needed. They had become too self involved. Everything had to go through the council, there was no heart, only duty. They denied these children the chance to live with their families. Jedi were forbidden to love or marry or have children of their own. Much like the Catholic Church commanders (and they've got some problems on their hands, don't they?).
The Jedi had essentially lost their way. To quote Stephen Colbert, "They're all fact, no heart." And in the end, their narrow dogma of what is appropriate and what is not lead to their own destruction.
I just wish that the PT made this line of thinking more obvious. What a great story plot! But no...it fell through. Damn CGI-fest.