Well rotation also is something a coach should take into account, no one is forcing clubs to go all in in all 3 competitions, it's not like they won CL or CI that season, they went far in both and ended empty handed. Allegri did a lot to help us win that first scudetto, he gifted us Pirlo, without him we couldn't have won it and their sour grape defeatist attitude after gol di Muntari was a big help too.
I don't hold him responsible for Milan falling to pieces after all the talent left the team, but in 11/12 he fucked up hard which affected his reputation.