I think the most glaring issue is that Pete seemed to have learned nothing from Sean, and is hell bent on just trying to use the same playbook instead of adapting to his current personnel. But, Sean's offense is all he knows, and he has shown that he doesn't even know it well enough to score points regardless of who is playing QB, despite having the best set of weapons that we've had in a very long time. Pete has never run an offense on his own at even a college level, let alone in the NFL. His highest coaching position in the NFL before coming here was WR coach.
I'm not really in a spot to judge the rest of the staff when it's the blind who is leading them.