Micky over there at the swamp is a wonder bag. Yes, he was the best Dortmund player last season even if he is somebody that is better against small teams than in the bigger matches - but he for sure only works when packed in cotton wool and has a big mentality problem. I expect him to be the next guy that returns to Dortmund.
Gündogan's only big problem is his injury record. Else I see him a little like Thiago at Bayern - they are similar with the positions they can play in, too. Both have a lot of potential to be that world class midfielder but due to injuries could only show glimpses of it.
About playing Silva, Gündogan and KdB together. Against small opponents Pep could play them together as a midfield three - but he might often use KdB on the wing, too. I do not think Guardiola will have that wing focus at City like he had it in Munich - there he had 2 strikerlike players that were able to convert high crosses, too.