For me, the single biggest flaw in the prequels is the complete lack of romantic chemistry between Natalie Portman and Hayden Christensen. It ended up being a major stretch for me to believe he'd even tell a white lie for her, much less betray everything he had known for years.
Chemistry between actors matters - it's a large part of why Star Wars was such a success in the first place, and why Star Trek was remembered despite being cancelled before season 3 was completed.