I personally hated the idea of the droids in the PT, but I do know of a way they could have fit where I would have been quite happy with the results. It would have been cool if the droids had been in the PT but never met the major characters. They had their own subplot where they would be able to happen to wander into areas right before or right after the main characters. But they'd never understand each other's motives or even see each other. So the droids could walk into a battle site after the Jedi were done and have their own comments and theories as to what happened. It would become a fun running gag that they'd always just miss the action. Then he could have had the droids in there as an interesting comedic device without having to worry about how it was going to integrate into the existing movies.