I do not doubt the Cobb AP claims. The reason not too many people have them is because Cobb kinda neglected the MS6 community and decided to focus all their efforts on Subbies, Evos and MS3s. That left the MS6 community very bitter, and we were forced to turn our attention to CP-E and Protege Garage. CP-e came through like our guardian angels and there is very high customer loyalty to CP-E because they stuck with our community when no one else did. Also, the biggest benefit of the Cobb AP is that is was supposed to control the throttle, which CP-e figured out and released a few months ago. With the CP-E throttle reflash, paired with the Standback (which people have had on their car for up to 2 years), the CP-E equipment does all the Cobb does and then more. Because of this, there is very little reason to switch from CP-E to COBB. Plus, most of the people who really want to modify these cars already have with other parts.
So, I do not think it is a reason of COBB being inferior, but just they are now late to the market and dont have the customer backing they once would have had.
You may want to read the MS3 forums because they released the Cobb AP for the MS3 maybe 6 months ago, but there have been alot for re-sale. I do not know the reasons because I try to stay out of that thread.