Went to Proto about 3 weeks ago and didn't really rate the food. They seemed a bit fond of chips. And the service was poor. They had a large Japanese group in and the rest of us were pretty much ignored. (Bread being brought only at the end of our main course for example...)
Found that the more basic places with a short menu were better for food on the whole - very fresh and service was better. Try Rozarij or Kamenice. If you like seafood they're hard to beat.
Didn't eat at Nautika or Orhan though Orhan looked as though it had the edge on location. Bit tricky to find though!