We'll see. I don't think there is much difference between them.
I also think that the result of the games last season, is a bit misleading. IIRC, Bayern dominated on Spain but couldn't score, while on Germany, Guardiola totally missed the tactics and Ancelotti scholed him.
Still, Guardiola is a fast learner in my opinion, and will do better if they eventually meet Madrid. I like how Madrid plays, but they aren't an unbeatable team like Pep's Barca. Simeone's Atletico is a very good example of that. Even on the final, Real was extremely lucky to win.
In an eventual match between Madrid and Bayern, I think it would be around 50:50 and if I had to choose the favorite, I would actually choose Bayern (don't forget the curse of the winner, so Madrid won't win UCL this season). Chelsea and Atletico are a bit below, all other teams are far below these two teams (unless BVB finds some form, which looks very unlikely at the moment).