I refuse to believe there is no way to alter an ecu. Is this ecu different than any other in the world? It took 6-8 months before someone broke the code on the VW 1.8T but after that, they basically took the ecu apart and put a piggyback chip on the brains. Then they figured out how to alter the ecu thru the OBD port. This way there is no physical change to the ecu, just different programming. I'm pretty sure the new mustang will have this port since I think its mandated by whatever OBD version your car has. What info has been given so far on the factory ecu? Like ford said the hardest part is the drive-by-wire throttle, which is no different than the 1.8T. It's a programming nightmare, not to mention a dangerous area to mess around if you don't get it right or have reliablity issues. Some ecu's if they see increased performance or figures(airflow, fuel, timing, etc...) will actually think something is wrong and try to bring the performance levels back to stock. Even basic bolt ons might affect the car in the wrong way. I'd wait for a chip before I did any changes to the cam timing, spark timing or anything else that the ecu will monitor. How is the spark system going to be, coil packs, distributor cap? I would assume coil packs with the way technology is going and considering everything seems to be ecu controlled in this new car.
If this ecu is really unable to be altered then companies will just design a stand alone. Which is a great tool but too damn expensive for the person that only plans on doing basic performance upgrades.