What is needed, in my opinion, is a standard methodology for interactive communications for audio/video electronics. Whether the medium is bluetooth, RF, etc., the data layer could be some XML-like EDI format that both sides (remote and unit) can interpret. This could also enable unit-to-unit communications, i.e. your cd player telling your processor what is playing or telling the remote to go dark when your movie starts playing and to light up when the movie ends.

If the standards are kept open, you could just purchase your favorite "remote" form factor from anywhere you want, perform some sort of "handshake" with the unit, the unit itself could store and send the remote all it needs to know (commands, codes, etc.), and voila! every company that charges $400 to program your remote would be out of business. I said "remote" in quotes because eventually I think we will go to some sort of universal personal electronics device (like an iphone) that would take on any "personality" you want.

I wouldn't be surprised if a company like Sony, who has a reputation for integrating their products in innovative ways, would start something like this.