I would say it was the apparent failure to plan for Fergie's retirement and to have a board with the courage to manage him out. GIll did many interviews where he assured us all that there was a plan and the club had learnt from past mstakes (the post Busby era). The problem I see was that the Glazers massively lucked out on buying the club with Fergue at the healm, most specifically his ability to squeeze trophies out of a fairly average squad that was not being invested in, They were then both too ignorant too in debt to him to manage him out. Bayern always decided when a manager went, no matter how long they had been there. I have never seen an explanation as to why Gill left at the same time, pushed or jumped. I suspect bit of both.
So bottom line we exactly followed the disaster of post Busby. Allow Fergie to choose successor, allow him to sit upstairs and be a constant presence around club, allow him to contiue to have a role in decision making. At the same time, allow the football structure, youth systems that the great man had put in place to fade away and leave us well behind our challengers.