Tone, Characters, Dialogue.

When it comes down to determining the "fundamental flaws", no one will really care about plot holes, or sufficient villain motivation - those three are what makes a movie enjoyable and memorable, and that's where the prequels fell short.

I've recently watched GoldenEye - silly and campy as heck, but AWESOME lines, slick characters, and just tons of fun.
Also shows what really matters in portraying villains - not so much their goals and motivations, but the personality. I still don't get whether Sean Bean wanted to blow up London while getting rich, or getting rich while removing the traces, I don't really care what the hell Famke Janssen really wanted aside from killing random people, I don't care about that General's political motivations... but they all had VERY memorable and entertaining personalities, and each did something that made the audience hate them and wish for revenge.

Did we have that with the Neimoidians? Or Grievous? I think they cut out that scene where he kills a hot Jedi with too much make-up.