I have a Pentax 645N system and a Fuji GS 645 Folder. I love both cameras and each is excellent in its own way.
The fuji is one of the smallest cameras I have and the images it produces has a special feel to them- very sharp and great bokeh. It has rangefinder focus and a built in meter (no auto exposure) and in the normal shooting position the frame is vertical. For a folder it is very sturdy and it's portability cannot be understated for a medium format camera- can fit in my jacket pocket easily. Also allows you manual focus which the newer AF models do not.
The Pentax is not huge but also will not go unnoticed and is pretty loud firing off a shot compared to a soft click of the fuji. It can fit into a relatively small camera bag with extra lens and accessories. The auto focus is decent but not like a quality 35mm SLR or DSLR. The viewfinder is awesome and manual focus is a real pleasure. Have many choices and high quality lenses to choose from. Handles just like a 35mm SLR and has great internal metering (spot, matrix, ect). Unlike the fuji, I typically have a more deliberate plan when taking it out- don't just grab it and go.
In the end both could suit your needs. It depends on what level of flexibility you desire, size consideration, and shooting preference (RF vs SLR).
I'm keeping both!