The differences are that P-FC has 20x20 maps and Nistune has the factory 16x16 maps. This really doesn't make a difference as the ECU will interpolate between the map points. So really unless you are making huge power like 600+hp and you need to stretch you map to cover a large load range you will not be at a disadvantage, and really an extra 4x4 points isn't increasing it dramatically anyway.
The Big Difference.
Nistune retains Knock Control where as P-FC does nothing to control knock except flash a LED light on your dash. So Nistune will richen you fuel map and pull timing out ignition map if a knock incident is detected but P-FC will flash at you while the engine is pinging it's tits off.
The cost.
Nistune: Board ~$250, Software/Licence ~$200, Cable ~$100.
Really all most people will need is the board, if you want to play (at your own peril) or data log then you can get the licence and the cable. Not sure whether the OBD2 tunable boards need the cable.
P-FC: ~$1000 second-hand, FC-Logit ~$450.
Without FC-Logit you can't do the things you can with nistune and the software.