There were more rifts in the franchise and less unity. A bigger split between the front office and the coaches. An incredibly awkward, low-power spot for Caldwell with regard to speaking for the team. The Polians' circle was a smaller and smaller one.
All that combined to give the organization a little bit of Al Davis Raiders flavor -- super secrecy, odd decisions and revelations, insistence on the rationale being used being unquestionable. Maybe you could make the case for borderline dysfunctional once you added the nepotism issue.