I've really come around to see the good trilogy that I feel is hidden in the prequel movies.
The base storyline should have been (and kind of was?) the gradual decline of Anakin into the dark side. This decline starts when he left his mom (a slave) at a young age to learn to be a Jedi.
The reason Anakin's decline doesn't feel right is that he was for 2.5 movies, a good guy with a single outburst of anger and an arrogant streak. Then for the last .5 he just flips for no apparent reason.
A better written and paced trilogy would have done a much better job at showing Anakin's decline through the trilogy instead of just a few moments that seemed out of character. The Anakin of most of the trilogy is a friendly companion to ObiWan trading witty barbs and having each other's back. There was no sense of decline on screen.
The overall story of the prequels trilogy is solid, it's just not translated to the screen well.
This is opposed to the sequel trilogy which had no discernable overall story.