Instead of Apple offering yet another remote control, or getting into the money-losing TV set selling business (I know, the phone business had a lot of losers and Apple's done fine there as well, but...), how about Apple keep the ATV a separate box, controlled in almost all cases by your iPhone (still sell the $1-to-throw-in remote control so it is accessible without the phone/ipod/ipad, but for all intents and purposes the iPhone is the de facto remote).
But, to integrate well with the rest of the stereo system ecosystem, allow the ATV to control the rest of the home stereo as well - turn on the TV, adjust the inputs and volumes on the receiver, etc. One way to do this would be to send out those little IR repeaters to place in front of things; another would be to tie into various wired control systems (doesn't seem to be any viable standard there yet, but perhaps Apple could champion one).
In any case, the problem with the home stereo is not too many devices, but too many remotes and too many disparate interfaces. That's something that is pretty close to Apple's wheelhouse, if not almost dead center. ATV should be solving the user-facing interactions mess.