While MUC is a very wonderful city, PRG is much more interesting. I had the opportunity to stay on the Hilton PRG club level last summer and the location is pretty good and the club lounge was one of the best that I have ever experienced anywhere. It is just massive and they have excellent service and food/beverage offerings. He was Diamond and I am not familiar with Hilton enough to know if your gold status will get you in?
I have made several trips to both cities and I suggest PRG, hands down.
If your post was just to compare hotel value, I have not experienced the MUC Hilton.