Previous discussions on this where inconclusive. I would like to start with listing the similarities and differences as I see them.
Similarities
Both are fully electronic.
Both include/have available an adapter plate for different cylinder heads.
Both have a computer interface
Differences
FP has an optional valve to automatically control the pressure
PT can read velocity and flow concurrently
PT has software that records a velcity profile and graphically displays it. It stores and organizes the profile by lift, cylinder, and head.
FP offers a variety of cylinder bore adapters. PT uses a bore adapter of other sizes.
PTs standard bore is pre-drilled for Ford and Chevy (however it is 4.03 at time when 4.155 is more common).
PTs bore adapter doesn't recommend drilling Chevy holes for adjoining cylinders. (How does that work for the end cylinders anyway?)
PT offers orifices in more different sizes: 3.0, 2.5, 1.875, 1.5 and 1.0 inches. FP has 3.0 and 2.5 inches.
PT black box can be used with other PT systems, if PT knows at the time of the order. Minimal cost savings.
Prices are similar. EZ-Flow base kit: software, black box, bore adapter, orfice, and some .125" tubing is $899. Some of the harder to find PVC pieces will add maybe $100. Bore adapter is $250. Upgrade to Pro software $200.
FP is sold a la carte. Control unit $499, tube with orifice $199, software $99, benc receptacle $299, bore adapters $99. Flow pressure management valve $299.
Pictures:
Mouse FP system:
PT EZ-Flow System and System Drawing
Port Analyzer Pro Velocity Map