The fatal flaw were the characters, because as a viewer I could give a rats ass about most of them. The only character I somewhat gravitated to was Obiwan Kenobi, but I could honestly care less about Padme and Anakin.
I still think the overall story of the Prequels was pretty good, but Lucas couldn't pull off the emotional part of 99% of the scenes, so the movies just felt very stale when you watch them.
Star Wars Prequels are a perfect reason why I don't go to summer movies anymore, because most are flashy on action and CGI and light on character development and story.