The other problem you would have is there is no media center control modules or drivers for 2 way IP control of an HTPC either in Total control or CCP. The best solution I can give you is something like Redeye by Thinkflood. If all your devices are IP it can control them all without an external box but you would need the Redeye module for IR. It works with Droids and the software has scripting so it is very customizeable.

For regular remotes I don't see this happening in the consumer world for a long time. To a techie they can't understand why everything isn't IP and on the network but in reality it is not practical at this time. Reliability is key and the whole system now relies on a network. If your network goes down so does all the TVs in your house. Also, consider the amount of tech support needed if everything was network controlled and how you the average joe would deal with routers, access points, Static IPs, Vlan, DMZ, port forwarding, etc. This one reason alone is why IR still exists.

What could be done and hasn't is the manufacturers to come up with IR and RF standards so their remotes could control all your devices. This could put the universal remote companies out of business and take a big chunk of money out of installers and programmers. HDMI did try with CEC but as any installer will tell you that is a joke.

Good luck in finding a control system. The Redeye might be a good fit.