I would only feel comfortable playing three at the back if BOTH Fernando and Fernandinho were in front of them.
In that case I'd go:
Hart
Sagna Otamendi Clichy
Fernando Fernandinho
Navas Silva Nolito
Sterling Aguero
Caballero, Stones, Delph, Touré, De Bruyne, Sané, Iheanacho.
Sagna and Clichy are both fullbacks who can play CB so they're calm and pretty good on the ball. Otamendi is ideal for the central defender role because of his tackling skills making him a tricky last man to beat. Fernando and Fernandinho sit in front of and cover the back four, when one goes forward the other stays back. Silva is the creative force in the centre with options all around him to receive from the Fernas or fullbacks, turn in tight areas and find one of the four attackers. Navas and Nolito being asked to track back and help out.
I feel like that could work as the Fernas can drop back to make it a 5-3-2 if need be. I could be wrong but I remember the Celta Vigo manager saying Nolito is good at tracking back and helping his defence, if he's not up to it maybe swap him with Sterling. When everyone is fit I'd still play that, but swap Sagna for Stones, Clichy for Kompany, Fernando for Gundogan, Silva for De Bruyne, Sané for Navas.
Genuinely this is what I would do, granted I actually know fuck all about how to manage a football team regardless of what I think. That is a very strong side and Gundogan and Kompany still aren't there. Definitely enough to win the league. Anyone else think this can work or am I being daft?