If compatibility is a priority and bandwidth isn't an issue, MJPEG is still the way to go and is by far the most common encoding I see in security cameras.
On the other hand you could get cool stuff from the video encoding hardware, such as access to motion vectors on the cheap: https://github.com/osmaa/pinymotion
I wonder though if the OpenGL ES3.1 compute could be used for this purpose on it.
