I think I'd sort of twist the 3-5-2 slightly towards it being a 4-4-2/4-4-1-1.
I'd have Lichtsteiner play more like an orthodox RB and get Asamoah playing as a sort of narrow LM, in order to help the midfield.
I'd also have Vidal or Pogba playing deep in front of the defence with Pirlo, so thay Juve have more power in there to give the defence better protection.
That should also make it clearer what everyone's responsibility is, rather than having two wingbacks loitering in wide area and serving no useful purpose.
The only thing would be that, with the system I'd be proposing, the Shakhtar fullbacks could have be left in space, so Juve would have to back themselves to deal with crosses properly. From what I've seen of Shakhtar, that would be a comparatively safe way of playing them.
Buffon
Lichtsteiner-Barzagli-Bonucci-Chiellini
------------Pogba-Pirlo-------Asamoah
Vidal--------------
-----Vucinic
Quagliarella
That would also open up the possibility of marking up against Shakhtar's 4-2-3-1 (assuming they play that):
Bonucci plays as a sweeper
Lichtsteiner marks LW
Barzagli marks CF
Chiellini marks RW
Pogba marks AM
Vidal marks Fernandinho
Vucinic marks Hubschman
Asamoah marks Srna
That would just leave their LB free, and Vidal could shuffle across to him and leave Fernandinho to Pirlo.
I'm not usually one to suggest reducing a game to individual battles like that, but Juve were so chaotic in the first game that the clearer and simpler the instructions are for this game, the better.