Lucas really needed someone to tell him "George, this is a bad idea because of X, but I get what you're trying to do. Let's try Y instead" when he was writing the prequels. Unfortunately, Rick McCallum was not that man, not that it was his job anyway. As producer, his job was to do the behind the scenes stuff to make sure the movie could be made, not to hold Lucas' hand through the writing process. And based on everything I've read, anyone at Lucasfilms who tried to so stuff like saying "please tone down the slapstick of Jar Jar" or say "make R2 and 3PO be together right from the beginning of the movie instead of Anakin making him" was shown the door, rapidly.
For good or bad, from ANH on, Lucas always had to bounce his ideas off someone, but by the time TPM rolled around he no longer felt he needed that. The core of the prequels is great, but he really needed someone who could say "no" but didn't. I don't know if it was an ego thing, or if George really doesn't play well with others, or if he just has trust issues when it comes to his movies, or whatever.
That said, I do enjoy the PT and see it as one long six part story. Yeah, there are some clunky scenes and bad dialog and phoned in acting, but that stuff is in the PT as well.