What are the main limitations on using the following setup to boost frames per second capturing?
You could get twice the frame rate if (big if) the taking times of the cameras were shifted by 1/2 millisec. In other words, the frame R1 is time stamped 0.0010 sec and the frame B1 is time stamped 0.0015 sec, and so on. Sync would have to be centrally driven, and registration would have to be perfect.

That leads to the problem that the frames from camera B would be horizontally reversed WRT the frames from camera R. This could be overcome, just something to consider when trying to register the images.