Very true. the thing with the JWT is that it's not tuned/optimized for YOUR setup and basically just adds more fuel and timing. not a whole lot of changes, and they run a bit rich. usually around 12.5:1 AFR. lean it out a tad and you can make a few more hp as long as the engine is healthy.
here's a dyno pull on my old Maxima with a JWT ECU: http://blehmco.com/pics/car/dyno_1_sm.jpg

The JWT makes a lot of assumptions about your tune and just goes for a little more power with nice stability. there's several HP to be gained by tuning an ECU to your engine..