The fatal flaw of the prequels is that Lucas directed and wrote them.
That's all it comes down to, really.
Here's a good thought experiment. Take all the plots to the three prequel films and keep them, keep all the sequences and major scenes, keep the exact same characters, played by the exact same actors, with the same crew, same DP, same designers, heck even the same major designs. Then, have the script written by Lawrence Kasdan and the film directed by Steven Spielberg.
That's it: that one change. Different director and writer.
That, my friends, is the prequels going from mediocre blockbusters to minor classics. The scenes have drama and purpose, the dialogue is interesting, characters become complex and likeable, and the acting becomes realistic, with real emotion behind the film, powerful emotion. You laugh, you cry, you hold your breath. All from subbing in two human beings behind the scenes.
George Lucas should have thought up all the major elements of the films and been involved in the story and the production, but he should have let people who could write write the films and people who could direct direct the films. He knows he's a bad writer and bad director; he admits it openly. The problem is that Lucas is a narcissistic control-freak, and that major character flaw was so strong that he decided it was better to make three bad films himself than share three good ones with other artists.