Kind of a late reply, but decided to add my solution for the record.
My home system uses Quartus Prime 16.0.0 Lite Edition. Just like you, it would get stuck at the Fitter 35% when using Advanced Physical Optimization. From the Windows Task Manager, I would get 100% CPU usage whenever the fitter (quartus_fit.exe) got to that point.
To solve it I went to the Compiler Settings, clicked on "Advanced Settings (Fitter)..." and disabled Advanced Physical Optimization (Off). After that CPU usage wouldn't go past 35% and compilation time went down to a few minutes.