Considering most home automation control units (AMX, Crestron, et al.) still uses RS-232 (serial ports) for communication I don't see that shift happening real fast. Not saying this is what a vast majority of people are using, just that the CE industry is slow to adopt new control standards. Very slow.
With HDMI CEC getting better and better you may see more and more remotes with some type of RF communication to one of the devices and that device relaying commands throughout the system.
Samsung's remote in the 8000 series last year was RF and paired with individual TVs. That was a fun surprise.