Why do you think Nocerino cost 500k? Or why inter happy loaned us Muntari for free? Or why guys like Mesbah or Emanuelson cost so little money? Do you think these guys are Milan quality players? The only reason they're here is because they were cheap.
This team has only two world class players. Thiago Silva and Ibrahimovic. Some very good ones: Abbiati, Mexes, Aquilani, Boateng, Cassano, and Pato of the previous seasons. And experienced (previously world class) veterans Nesta, Ambrosini, Van Bommel, Gattuso, and Seedorf.
The rest are just not fit to start for a club like Milan.
Now the veterans have lost their legs and shouldn't feature much if at all. Mexes, Aquilani, Boateng, Cassano, and Pato all have been injured much more than they've been fit this season. This means the only Milan worthy players who have been consistently available for Allegri this season are: Abbiati, Thiago Silva, and Ibrahimovic.
And even Thiago Silva has missed the most important part of the season. So how do you expect a coach to win with those conditions? He has to play the Nocerinos, Antoninis, and the Muntaris. The fact that he's competed for a whole season with that level of players shows his quality as a coach. These guys are mid-table level. Milan is 3 points off the top.