Internal Lufthansa surveys are showing that MUC Crews are rated much better than FRA Crews by the customers. A few days ago I had the chance to compare (FRA-PEK / PEK-MUC) and I agree completely. Also the A340 is much nicer in F than the Boeing 747. Seat is of course the same but the whole atmosphere is much better in the Airbus. The Purser even gave us a tour through the galley and the crew-sleeping room in the lower deck.
And for the lounges: The Terminal in Frankfurt is not as good as it was before, while Munich was fantastic again. If you don`t mind that your table is not cleaned for more than one hour, you are not asked if you want something to drink and that your transfers get mixed up however, than the Terminal in Frankfurt is still a good alternative to MUC...