Dude, being the director doesn't mean he gets the final say. Remember NewLine had an "executive producer"on the set to make sure the movies are made to be cookie cutter eough for mass appeal. He's even in the frigging control room when they did the final mixing and editing. Besides, they are not given a blank check for the production. Several things PJ would have liked to have filmed for the movie (Gandalf's battle with the Balrog from the dungeon to the mountain top, for example) didn't get shot because there simply wasn't enough money for them.
Face it, the movies could have turned out much worse... like the Dungeons and Dragons movie.