Honestly the plots of all three of these movies are relatively straightforward. It’s the execution that muddles them. I kind of differ from a lot of people here in that I think 99% of the problems with the prequels are execution problems, not conceptual ones.
Well Anakin being an annoying jerk instead of good person was a conceptual problem. And him being an annoying jerk is pretty much the only real problem of PT as far as I am concerned. Of course bad acting and bad dialogue concerning his character amplified things, but in the end it was a conceptual problem to begin with.