The big difference is in Federer's movement. That is the root of all the problems. He is a lot less fluid, explosive, and athletic now than he was in his prime, and that results in a significantly worse baseline game. His forehand's backswing has been abbreviated to compensate for the decline in movement (so he can take it even earlier to compensate for the lack of movement) but this results in a shot with less spin, power, and consistency. Serve has definitely improved, backhand I think has improved technically but may be worse overall due to the reduced movement.
I'd say movement (especially to the right) and return of serve, Fed used to be able to frustrate any big server by getting crazy amount of balls back.