George made the lousiest decisions when it comes to the storytelling of the PT.
TPM has no great story to tell at all. The political intrigue of the Naboo invasion frankly isn't very exciting. The film introduces the badass who may have turned into the younger generation's Darth Vader, only to kill him off after about five minutes of screen time. The Trade Federation never come off as threatening either, since they're depicted as blundering idiots who wouldn't even be able to tie their shoelaces.
AOTC is better, but Anakin's character development - the supposed backbone of the film - is ruined because of Hayden's woody acting. Anakin is a whiny asshole from the beginning and doesn't come off as Obi-Wan's best friend or a great warrior. When he breaks down after the Tuskin Raider massacre, it's hard to sympathize with him at all. And when he hits on Padmé, he has about as much charm as a child molester. The script doesn't help him much either. "Everything here is soft... and smooth." Yeah, unlike your moves, creep. When the Clone Wars commence and the film finally gains real momentum, it's over. You want to see the Clone Wars that Luke is so curious about in ANH? Go watch a shitty CG film. That's like making a WWII film that ends right as Poland is invaded.
ROTS is actually pretty decent, in my opinion. I may be in the minority, but when I rank the films, this usually comes in on a second place after ESB. If it has any major flaws, they are to be found in the previous films. If Anakin was never sympathetic, who's going to care about him turning into Darth Vader? This is particularly frustrating because this film had a lot of moments that showed that Lucas can still be a great director. The "Order 66"-montage is brilliant and actually surprisingly emotional, considering we never really got to know any of these Jedi in the first place. The scene in which Anakin seems to communicate telepathically with Padmé across the Coruscant dusk is another great scene, mainly because of John Williams finally taking a chance with the soundtrack. Anakin turning on his lightsaber, startling the Jedi youngling is such a simple moment, yet it's among the most powerful of the PT. No elaborate CG-environments can rival the sense of dread that you get from this shot and I really wish more of that attitude had gone into the making of the PT.
Of course, ROTS still has its flaws. General Grievous is a dumbass with bronchitis, the romance between Anakin and Padmé is still awkward, the film introduces the gaping plothole of Leia remembering her mother, the incredibly idiotic "NOOOOOOOO" etc. But I don't think the flaws are as distracting as in the previous films, and all in all, it was certainly the best Star Wars installment since ROTJ.
It's a shame the rest of the PT just wasn't as effective because of Lucas' ham-fisted director/writer/producer-combo.