Ernie seemed to have lost the dressing room, and had signed players to play a specific formation and tactic that, except for half a season with Burns on fire, simply didn't work. He basically put all his eggs in one basket and when the bottom fell out of that it was smashed eggs everywhere. I think you can totally blame him for a lot of that - there is no excuse for a recruitment strategy which left us with Lia, A-Rod, WeeMac, Finkler, and Roly - all central midfielders of some kind and all either highly paid or imports or both. That's 5 players trying to fit into at most 4 positions (and only if you play the hard-to-pull-off 4-4-2 diamond or box midfields and cede any attacking width). Meanwhile we had no quality traditional number 9 and no genuine backup for either fullback position.
It really isn't surprising that we never really looked like a cohesive team consistently in the last couple of seasons - quite simply, we weren't. We had talent on paper but no way of making it work together.