Despite DBs assertions that the L2 AP was great, that wasn't a view shared by the majority of line pilots. The collective coupling was very slow to react to required changes and then had a habit of overreacting in an attempt to play "catch-up" and could cause momentary overtorques. As the data in the AAIB report indicates, most crews would chose not to use the collective channel i.e. only use 3 axis coupling.
The choice of 3 axis rather than 4 axis coupling wasn't itself a fundamental mistake, it was the choice to couple altitude to pitch rather than speed. The lack of speed monitoring at 80 KIAS and below was the final hole in the Emmental.