Wouldn't mind seeing him used ahead of Marchisio and Khedira:
Pjanic
Khedira-Marchisio
I think we can gain more value out of having Pjanic in the centre of the field instead of having Khedira higher forward. He needs the ball more, and he needs to be more advanced and he needs to have more cover. At this point, Marchisio and Khedira are not huge offensive threats so I would be fine with both just settling in front of the defence.
When Dybala is healthy, I don't really like how he's so far from Pjanic when Pjanic is at LCM. They are never combining. If Pjanic wants to hit a pass to Dybala, it has to always be in the air.
And he can't get any space between the lines playing on the left. You see this problem with #10s all the time. They lose a lot of effectiveness if they are playing in line with their other CMs. They have to be in between the striker and the CMs.
You could play these 3 CMs like this in the 3-5-2, you could play it in a 4-2-3-1 (with Dybala as an inside forward RW), or in our current state with Cuadrado and Alex Sandro on the outside.
I know Allegri said he tried Pjanic at regista because he wanted him in the centre of the pitch, but I think this solution makes more sense.