BarFury, if you have a little time on your hands.. try reading this post.http://www.furyforums.com/forum/fury-tech-performance-chat/850-exhast-pipe-changes-fuel-management.html
To answer your question which one is better?
Without an independent study conducted I don't think that can be answered.
CobraUSA recommends the Fi2000 with their pipes.
Some people went with the Power Commander V since it has configurable maps.
Fuggin Fabrication developed their controller and Dyno their pipes and air cleaner setup
The next variation is the Auto-Tune controller when coupled with a O2 sensor is suppose to compensate the fuel mixture.
All in all, everyone one of these products adjusts the amount of fuel sent to the engine by changing the output to the fuel injectors.
Stick a nice big air cleaner on the Fury that sucks lots of air in and you will get more air than fuel. It will run hotter since it is now getting more air than fuel.
The programmed (PGM-FI) with automatic enricher circuit with a 38mm throttle body is programmed to work with the factory air cleaner and not the aftermarket one.
With a factory program set to support the three-dimensional mapping with two spark plugs per cylinder.
(My understanding of the 3 dimensions are throttle position, gear position, and timing. I may be wrong but I couldn't find a clear explanation other than it's marketed on every Honda product including watercraft.)
The aftermarket Electronic Fuel Controller units basically intercept the normal fuel injector signals and apply their settings instead of the factory.
So which one is better?
I think all accomplish the same result with some having more programmable flexibility.