Switch from 4-4-2 to 4-2-3-1 gives him less control on the game (and more to Silva), especially against an attacking right back.
Fernandinho doesn't cover as much ground as he used to, wingers have more defensive positioning duty.
Millner isn't the answer to everything - looks good playing 45 minutes every two weeks when opponents are tired, wouldn't have the same energy playing 80 minutes every 3 days.
Without Toure, Nasri&Silva still managed to pass their way to the goal in the second half, amazing stuff really.