I do not think a 541 is bad against City but United deffo have an issue with cohesiveness in their lines. Once the front 3 is passed, the two DM are all alone against a sea of midfielders. There is not much they can do then.
I think a simple 4231 could work well if he put Cavani on a wing and another winger that can track back. Just tell you wingers to play narrow to force City on the outside. Keep the double pivot and Bruno-Ronaldo but they need wingers who are better at defending when out of possession
Im sure Pep tried to go for Kimmich

He loved dude when he was at Bayern.