I think it was the 4-4-2 diamond shape against Germany. At least from what I recall. Prandelli only used the 3-5-2 in the first few group games due to injury. The problem with the 4-4-2 diamond, while the match remains scoreless or behind against a team like Spain is that it is quite a narrow formation, and SPain was playing with that false 9 look, quite wide. We conceded from wide play quite easily in the final, they stretched us out so easily. Playing Chiellini as a LB in a 4 man defense is absurd and should never have been done against Spain. The 3-5-2 was the perfect formation against Spain as it has the width to not be so susceptible to their attacking wing play, that's why we did so well against them in that group match.
I like the 4-1-3-2 against a team like Germany or Argentina. Most other sides in the tournament really. Even the 4-4-2 can work. Just not Spain. Perhaps not Brazil either.
Bonucci is in terrible form right now, but if he can get it together come WC time, I prefer him in that role. When he is playing well, with mistake free football like he did much of last year with Juve, he is an excellent choice. Otherwise De Rossi is fine.