Think he should just play his natural position, inverted attacking midfielder cutting in, I also think Sterling should as well, Pep said it perfectly in his press conference that he thinks Sterling is better running at defender through the center than stuck out wide, and this season we have fullbacks who can stretch the pitch, with Mendy fit this formation should be devastating:
Sterling----Jesus-----Bernardo
D Silva----Gundogan----Kevin
Mendy---Stones----Kompany----Walker
We used this last season but this formation is more like a 4-3-2-1 than a 4-3-3 with basically 5 midfielders, Sterling and Silva would cut in, they obviously also have wide attacking duties as well.
I think Sane could rotate with either Bernardo or Sterling, in RW he can make run in behind to score cutting in or on LW crossing to the other forwards. Honestly, I don't think it's a stretch for Aguero to rotate in any of those spots as well, he is not a winger but this formation uses inside forwards which Aguero can handle considering he has great link up play.
I think if Mendy needs rotation then you can put Dinho there, but have Sane as LW and instruct Dinho not to attack and stretch but allow Sane to do that, Dinho's fault as LB are when he pushes up and doesn't have the pace to go back, and Danilo can rotate with Walker.