If anything I'd say the hypertech is nice since you can always go back to your original stock settings if you have to. Once you flash a pcm then it's like that until you reflash it correct, since it is a reprogramming of the computer.
It all depends on what you are doing with the truck. If you are just adding a few bolt ons it great. If you decide to really tear into the motor and add a cam,heads, supercharger, etc... a flash is a must. The hypertech or superchips is nice because you can always go back to stock. If you are looking to upgrade the motor i would go with a flash to get the best gains out of the truck.