There are many pros and cons of both the cobra and the power commander.
Is anyone familiar with Dobeck Performance who makes fuel tuners? (EJK, TFI, they just released a new autotuner called the AFR+) The owner of this company founded Dynojet and invented the dynomometer. the tuners are affordable, easy to use, have on the fly tuning, do not require a dyno or a computer to tune. Dobeck Performance also manufactures controllers for over 80 private labels. you have probably seen the tuners with intake & exhaust kits, in turbo kits and other big labels like Wiseco & FMF.
I have researched the controllers on the market and heres what I'm finding.
The Cobra autotunes to 12.5 AFR only during acceleration. 12.5 AFR is a good AFR value to target but is not ideal for all situations. The CVT tuning at 80x per second is just a gimic with the power pro. Most processors inside any controller are taking readings at 80x per second.
In conclusion, the power pro is a good tuner, but you are stuck with 12.5 AFR only autotuning during acceleration.
Dyno time with the Power pro wont do any good because you cannot change the 12.5 AFR it targets.
The power commander is your most expensive option, but has been the most popular because Dynojet was the first company to develop tuners. They also spend a lot on marketing and are well branded.(hence their popularity)
The power commander w/ autotune is almost $900. This does not truly auto-tune. Its what is called automapping. The PC5 with autotune takes readings from your motor using the wideband O2 sensor and makes a new map for your bike. Once again the auto-tuner only tunes to 13.3 AFR which is a good AFR value to target but not in all situations and rpm ranges.
Dyno time is expensive and your tune up is only as good as the person tuning it. If you do not have the autotune on your power commander you will have to spend money on dynotime, or download one of the maps that are out there. Once again, you are stuck with a map until you download a new one or spend more money on dynotime. Your map would need to be changed anytime you put any mods on it or are in different climates/elevation.
In conclusion, Power commanders are expensive to begin with, will continue to be expensive with dyno time, and are not easy to tune because you have to download maps or have new maps made anytime you want to change something. People will continue to tell you to buy the power commander because thats all they know and its a popular tuner
Dobeck Performance tuners can be tuned on the fly, are about half the cost, and will give your bike a good tune up with the preprogrammed map straight out of the box.
Their new AFR+ autotuner uses an AFR gauge and wideband O2 sensor to autotune to any AFR value from 9.5 -16.5 AFR
You can set up your controller to target any AFR value for both the acceleration and full throttle fuel ranges (12.5 is good for full throttle, 13.3 is good for acceleration, going leaner can get you better gas mileage if its something you want. Each engine will run optimally with a different AFR value. engines with cams tend to like richer AFR values
The AFR gauge lets you know how your bike is running at all times. It makes it easy to find flat spots, lean/rich spots, and diagnose other issues like exhaust leaks etc.
It doesn't require dyno time and can be tuned on the fly for whatever driving style your feeling. If you want to race, Target 12.5 AFR to go gear for gear against the bike in the lane next to you, or get good gas mileage and target 14.5 AFR while cruising on the highway to save on gas.
Those are my findings after researching fuel controllers. If I am wrong on anything I stated, please clarify. I will be happy to answer any other questions.