I think the storylines for TPM and AotC are fine, but the screenplays are what drag them down. The dialogue is horrible, the pacing is bad and drags horribly in spots, and TPM suffers from a very peculiar defect in which one leg of the multiple angle end battle scene has no tension or drama whatsoever (Annakin "accidentally" wins the battle for everyone? :\)
The acting isn't really that great, but as others have said, that's more likely a product of bad directing with bad material than actors who can't actually act well. Annakin was also spectactularly miscast in both movies -- one, because nobody believes that this little kid and this teenage queen could possibly have any chemistry, and in the second movie because nobody believes that a skinny, petulant and bratty teenager is going to become Darth Vader in a few years.
There were some early rumors that Ryan Phillipe was being considered for the part; my wife and I firmly believe that if he had been cast as Annakin in all three movies, it would have worked wonders. He's a good looking guy, but very masculine, and the ability to pull off the attractive and seductive, but also somewhat creepy bad boy that Annakin needs to be.
On the other hand, although I'm certainly not too fond of Jar Jar Binks, I don't consider him to be the movie breaker that many obviously do.