You might want to check out Sniper Tuning. They have a package called "special forces" that allow you (the end user) to make changes as you add/change modifications. I know I keep pushing these guys, but the guys behind the company are the guys that have been working behind the scenes at the big operations like superchips, diablosport, and hypertech. You actually make changes with your home computer or laptop and download it to the flash programmer. You can even change things like WOT shift firmness and shift RPM, add or take away timing and adjust the mixture to suit the modifications. If you need anything really special done like part throttle shifting or really wild combinations you can have the changes done by them or someone with the dyno shop version software (like me) and changes can be done via email or in a dyno shop.
They are the only ones really offering this kind of programmer and you wouldn't have to buy any more hardware to make changes later.
Matt