The problem with bluetooth is limited adoption in the home theater market - the only components you're likely to see in an entertainment center that offer bluetooth are the PS3 and an HTPC. Likewise, all of the third-party and OEM remotes are either IR or IR/RF, so there's no support for providing the pre/pro with a good universal remote or even a good standalone remote that uses bluetooth. At this point, for every person who likes the PS3's bluetooth remote there is at least one other person who is annoyed by the fact that they have two remotes instead of just one because their universal remote can't control the PS3. In fact, the lack of proper IR remote support is one reason that I held off on getting a PS3 as a Blu-ray player.
Bluetooth has the potential to be a good remote control interface, but I don't think we're going to see it happen on a large scale any time soon. For one thing, it is going to require remote manufacturers (companies like URC and UEI for both third-party universals and OEM stuff, plus companies like Harmony and Pronto for third-party) to provide some bluetooth remotes - and when they do, the universal remotes will need some way to be programmed to control multiple devices even though the convenient "learning" function will be taken out of the equation when we lose IR. For another thing, we'll need some bluetooth-to-IR hardware (receivers with emitters) or IR emitters in the remotes to support legacy hardware while bluetooth components work their way through the market.