Both setups have advantages, it mainly depends on what you are doing. For an NA setup, the VEC-3 has NO advantages over the flash tool, and in fact many, many, many disadvantages. The only disadvantage to the flash tool is that since it is based off of the OEM MAP, it cannot handle boost- YET. a simple re-write of the software with a new 1 or 2 bar MAP sensor and it could easily handle boost.
The best thing going right now is a flash tool AND a VEC-3 for a boosted car. the engine can be completely re-mapped with the flash tool, and the ONLY thing that the VEC-3 will be doing is pulling basic timing and adding fuel in one demension only, IE boost. The VEC-3 has many disadvantages when it comes to open/closed loop transitions, injector scaling, etc... all of which the flash tool can take care of at the source.
Just as an example, I have a car here right now running 96lb Peak and Hold injectors.... with the FACTORY PCM controlling them in their entirety... these are BIG injectors which the VEC's are not capable of controlling without a host of issues coming into play. There is a VEC-3 in the system, but it does not handle trims, scaling, or anything other than simply adding fuel and pulling timing- period.
It all boils down to this: Short of Boost Control and Traction Control, the Flash software has just about every capability as an AEM, but remains OBD-2 compliant, and there is NO wiring. Its capabilities will be expanded in the future as new software is added, and you can expect that boost control may be in the future. It is probable that the new flash software and a racelogic unit will replace the AEM's in their entirety when the software matures. There are a multitude of spare pins and unused tables in the PCM, once they are mapped, it is likely we will have some "blank tables" in the software for adding various functions based on other tables already contained in the PCM programming.
I have personally dealt with all of these systems, and I can honestly say, the flash software is the ultimate answer to the question, it just hasnt been completely finished yet. If you have any specific questions regarding the flash software and its capabilities, please let me know. I am a dealer for SCT, and have DCX (Viper) flash tuning capability, so I can tell you exactly what it can and cant do. I have also been helping SCT mature this software as fast as possible, as it appears I may be pushing this software to its limits first.