It is likely that NHTSA will mandate, or Congress will pass a law which requires that automakers who use Electronic Throttle Control Systems (ETC) must have brake override logic, similar to the software update that Toyota is releasing as part of its recent unintended acceleration recall.
As this feature becomes more widespread, two-foot driving will become a little bit more difficult. The two-foot driver will find that if they overlap brake and throttle pedal application, that they will get abrupt reduction in engine torque, and therefore more abrupt deceleration, as the ETC system slams the throttle closed to reduce engine power. In order to drive smoothly, they will have to take the time to lift off of the throttle before pushing the brake, giving up much of the perceived advantage of two-foot driving.