I think Lucas did a horrible job making the prequels as mythological as portrayed in the OT. He even made scenes with Yoda landing on Dagobah, as if nobody has any imagination left or something.
And the pushing out of the Skywalker twins and Padme's death were also a bit unnecessary.
But like everybody else, the clones being on the side of the jedi was really what screwed it up for me and I didn't even notice any war.