It was fairly well known that season three was a nightmare for the writers. Behr left due to it, and had to be really talked back into Trek. Piller gave interviews were he would talk of how his plate was full of just constantly rewriting, script after script after script.
Now the head writer usually takes the final pass and usually uncredited, but usually they make little to some cases no changes. Piller talked about the heavy amount of rewriting he had to do on almost every single episode. Thats why he was very seriously thinking of not coming back for season 4.