Most of this tracks to me tbh. Bill was such a presence and ultimate final say in every bucket of the organization that it was way too hard to give anyone a fair evaluation without the caveat of "Bill got to make the decisions and I couldn't challenge him all that much". It's hard to know if the scouting and personnel department sucked when there were so many stories of Bill overruling them. It's hard to make an evaluation on BOB and Klemm when Bill is telling Klemm to coach the line a different way than he wants and is filling BOB's staff with guys BOB doesn't want.
It sounds like Kraft had two many scenarios of asking people "why is your part of the team not doing well" and he kept getting responses to the effect of "I didn't want it this way, but Belichick gets the final word and I didn't have a leg to stand on to disagree". So you had Bill running the organizationally too close to the vest (which makes sense when you realize we haven't had an official DC for years and last year didn't even have a real named OC). If there was one problem, you could blame one problem child and move on. But there were so many problems where the excuses were "ask Bill why he wanted it that way" that there was just nobody else to really blame anymore. And as things got worse, you had Bill saying uncharacteristic things like "well look at the past 20 years" when he got questioned. And in the end it just became untenable.