Ok, in order to help people make a better choice between the DynoJet Power Commander V (5), the Cobra Fi2000 series (PowrPro specifically) and the Guhl Motors ECU reflash. I am attempting to make this sound as unbiased as possible using hard, long known facts and little personal preference.

I am more familiar with the PCV than the other two options, and the PowrPro documentation is limited and all the links are broken including the testimonials and specific installation instructions. The ECU reflash is fairly well documented for the performance and options available and is a good choice for the 'i never change anything on my bike' crowd.

To explain a little more...

The PCV is in itself almost a full blown stand alone ECU itself, with the exception that it is added onto the existing EFI system and with the right model (16-025) removes all fuel and spark (timing) control from the ECU leaving things like radiator fan and cold start idle control to the factory ECU. You can load custom maps from any source, fellow user, dyno shop or DJ themselves (although i find those maps are pretty conservative). If you get one from a friend, it can be made using dyno time or the AT200/300 add-on modules. Without these two options, adjusting the map itself is pure guess work and you need to be careful. With the PCV you can eliminate the 100 mph limit on the US bikes using the included RevXtend feature (which changes the red line to 5400), or sign a waiver releasing DJ from liability and get a lofty 6100 rpm limit. You can also adjust the timing for every 250 revs completely independent of the fuel table.

The Cobra PowrPro lauds itself as a 'install and forget it' tuner that "analyzes the injector and crank sensors up to 80 times per second and makes the appropriate adjustments" but does so without knowing how much air is flowing through the motor. Sure, it can be programmed for 1312cc's of total volume, but it cannot know the actual airflow or the speed (due to different filters and their inherent restrictive natures). I do not feel this is a good choice for anyone to use based on that sole reason as this could lead to melted pistons if you run too lean, clogged valves if you run too rich, etc. Ask any tuner, any engine builder, any drag/circle track/circuit racer how you can tune a motor without knowing how much air is flowing through it, so that the proper AFR (air to fuel ratio) is achieved and they will tell you that you cant. There are 3 ways to achieve this: using a specific CFM rated carburetor and many jets to swap out (major math involved and more so if you have to adjust for humidity/elevation etc), MAF/MAS (mass air flow sensor) and O2 sensor. An O2 sensor can be used with carb or EFI setups, although a carb'd setup requires a manual adjustment whereas EFI can adjust on the fly with the ECU/ignition control module of choice. The only way i would recommend this unit is if you get your bike dyno tuned, which honestly, kinda defeats the point eh?

EDIT: I believe also, that the PowrPro only ADDS fuel, but cannot take it away and there are many times where having a leaner mixture is preferred.

The ECU reflash is a very good option. It allows the ECU to work the way it was designed and can be used to load custom maps (like ones built with a PCV w/Autotune setup) and could potentially allow the bike to perform 'better' overall/in concert as if the settings were that way from the factory. As far as i know, the only drawback is if you change the airflow, you may need to change the settings which requires a reflash (downtime) but without your bike being dyno tuned and the map from that loaded directly into the ECU, its still a guess based on your actual setup. 

As far as recommendation is concerned, my honest opinion with no stock invested (either by actual stock, or compensation from anyone) in order of 'safest' to 'most dangerous' with the irony being the order of least expensive to most expensive also:
1. PCV
2. ECU reflash
3. Cobra tuners

Now, for a spread sheet showing the major differences between the 3 and available options