If you have reason to stay near the Munich main train station, I highly recommend the Schiller5 Hotel on Schillerstrasse, just a block outside the station. I know this area is not considered the nicest, but the street is fine and the location so convenient. The hotel itself is great---very friendly staff, and a lovely modern room. I booked a prepaid rate in advance and got a great deal on a rooftop studio--- a very large room with balcony, huge bathroom, and kitchen facilities ( fridge, microwave, and stovetop).
We had only one night in Munich, arriving and departing by train, so the near-station location was a perfect choice. But if returning to Munich, I would book there again even for a longer stay, as the room was so nice. Plus the nearby Geisel's Vinothek was a very nice place for a light (and late) dinner.