Much like Chelsea they have struggled domestically, I know. In Chelsea´s case their most important players are not top class any more. Lampard, Drogba, Cech, Terry - neither of those are top class any more, but most of them will still play. If you then factor in that Torres is their option to Drogba, that Cole has been poor the entire season basically, and that at least one of Cahill or Luiz will play it doesn´t get any better. They are just not a very good side. 🙂
If you look at Bayern on the other hand, they are just getting Schweinsteiger back, have a top class goalkeeper in Neuer, have top class wingers in Ribery and Robben, and a striker in Gomez who is very good within Bayern´s system. I like Kroos, Lahm and Müller a lot as well. Unlike the other German teams in the CL, Bayern also have the experience from constantly being in it to draw from.
Personally I think Bayern would beat Chelsea quite easily, and that Milan would be a toss up.
