Last time I got a car from MUC (summer, Sunday afternoon) a few of the companies had very, very long lines. I don't remember the companies, but they were major names (Sixt, Hertz or Avis).
I would look into the programs that might allow you to skip the lines. Not sure if any have the 'go straight to the cars' at MUC. You could also consider making two reservations and going to whichever has the shortest line.