The problem here is pretty clearly deeper than the decisions made last offseason (Shatkins is 100% right that this wasn't fixable with a few offseason moves). It's also deeper than a choice to value run prevention. The team has to identify why almost nobody in the org is playing to their abilities, and why they've been a bottom of the barrel team when it comes to acquiring young talent and then developing that talent into quality major leaguers. The only solution here is poaching someone from an org that does things properly and giving them the autonomy to overhaul the baseball ops side of the organization however they see fit.
Atkins will probably learn from his failures here, go work for the Dodgers for a couple of years, go to St. Louis mid-rebuild, spare no expense on cutting edge nerds, and turn them into a dynasty.