I think Bayern would be favorites in any of these games for sure. And they are brutally consistent as opposed to the likes of Chelsea and City who like to drop points against minnows like Sunderland for example. That is why nobody in Germany is able to run close to them at the moment, they have so much squad depth and experience in the team that they keep on winning games.
CL and League is an entirely different thing, I mean Schalke beat Arsenal in 12/13 so does that mean they would compete for top 4 in the PL?
Dortmund top the group again ahead of Arsenal despite struggling badly in the League, what conclusion can we draw from that?
I'm talking more about the league (even though i previously used CL examples). Bayern would not be able to maintain their consistency in the Prem because they would have too many difficult opponents to deal with. Its not hard to do so in the Bundesliga but not quite as easy when you have the likes of Mourinho, Sergio Aguero, Diego Costa, Wayne Rooney and others to deal with multiple times each year.