The problem isn't the 4-3-something, it is Allegri's choice of players to execute it. That extra player in the final third hasn't been consistently used and often we see vidal play that role just so Allegri can fit in Pirlo, Marchisio, Vidal and Pogba on the field at the same time. In addition, Allegri isn't fully committed to having a creative player in that role.
Pereyra isn't all that great, he manages to do good work but lets himself down in that final stage whether it is a poor pass or not taking a shot when he should...and if he does take that shot on goal it isn't very promising.
I think we also suffer from the 3-5-2 system where players like vidal and pogba were able to push up more in midfield as we had the trio at the back covering us. Not sure whether it is just a natural instinct from the Conte era but it does expose us against teams who are good on the counter. Scares me to think of what Dortmund could do.
For me I think Allegri just needs to appoint a starter for the extra player in that final third. Definitely not Vidal, he needs to play as he has over the years. Pereyra may offer us more if given a handful of games to start in that role and make it is own. Giovinco is gone but why not try Coman?? Or why not use Tevez and Morata alongside Llorente? Morata has pace, he can dribble, I think he has more to offer than just be cover for Llorente.
Last but not least, we suffer with Pirlo starting. Love the man, he is a legend but he needs to be told.
buffon
lich bonucci Chiellini ??
vidal Marchisio pogba
Morata Tevez
Llorente