I'm pretty sure the BC296D can work from control frequencies only as well, at least if you beleive their manual, I haven't tried it myself.
I've heard that the main advantage of the Pro-96 is the capacity to store and recall more trunk systems, since with the 296 you're restricted to one per bank and there's 10 banks so you run out real fast but on the Pro 96 there folders in which you can store more than one set of banks?