I'm going to weigh in and say that if you're a city person, I doubt you'll find Munich overrated (but you might wish you'd spent your whole trip in Berlin!)
I was underwhelmed with my first couple visits to Munich because the touristy stuff isn't that exciting yet everyone treats it like a tourist town. It's when I appreciated it as a city in it's own right that I grew to love it. Now it's one of my favorite places to visit.
One thing, why do you have to do Munich then Salzburg if you're flying out of Munich? Have one long travel day from Berlin to Salzburg, then head back and visit Munich at the end. Makes a lot more sense.
Don't sleep in Munich's museums, they have among the best collections in Europe. The Alte Pinakothek has Duerer's amazing self-portrait, probably my favorite piece of art in the world. The Glypothek is a truly impressive collection of Greek/Roman statuary, which should probably be returned to where it was stolen, but for now it's nice to see it all in one place.
And while you have to have some Bavarian food and see the main sights, I recommend getting out of the center for a bit and visiting Schwabing or the Glockenbachviertel neighborhoods, especially for more food variety when you're getting sick of German, bars, unique shopping, and just a cool atmosphere.
Personally I think one full day in Salzburg is enough to see the city itself, but if you want to do anything else (sound of music, Eagle's Nest/Koeningsee, Salt mines etc) you'll need that extra night. I like Salzburg fine but I don't think it's worth QUITE the degree to which people here sing it's praises.