I see this criticism leveled a lot, and while it's very valid, what Piller did say is that he had to create drama outside of the main cast, which he and the writers did. While it's unconventional writing to say the least, it still worked.
Indeed...and Pillar also said in one interview that what Gene was trying to do was push the creativity of the writers. He appreciated after initially feeling hand cuffed. He realized it was forcing him to think in new ways and not be lazy.