Problem is he has 5 good central midfield players, so it's the most suitable formation from that perspective to allow Asamoah to play. He does a fair job there, but we are still imbalanced as an attacking force, with him and Lichtsteiner. I'd also rather Asamoah played there than face what Isla does, as he is a very good player.
The 3-5-2 also allows Barzagli-Bonucci-Chiellini to play, which works very well for those players and the team, especially Bonucci. In a central two you lose half of his better attributes and expose his weaknesses.
So I don't see how the 3-5-2 is being used because of coach preference, especially considering it's not a system he had used before. Now there is an argument to go with the 4-3-3, with the entire left side of the team missing, but then you are also missing two key components for the front three; a fit Vucinic and Pepe.