Lack of open standards
I would use a HTPC, but there is a real dearth of open standards. I don't want to be locked into one hardware vendor, software vendor, or service provider.
If I have a HTPC will I be able to get HD source from cable? From satellite? Will it be able to play downloaded movie when they arrive? Will it play all of the umpteen DRM music and video formats? Will it be able to control everything in my component stack?
Not much of this is really the fault of a HTPC. The whole home theater industry is at fault for sticking with proprietary standards and DRM (which does nothing to stem piracy, it just makes everything more difficult for us law-abiding cash-wielding customers).