In my opinion if you asemble a PC that is fully compatible with Linux you will have few problems installing a distribution like ubuntu or xbmc-live. I think that in this case installing Ubuntu is simpler than installing Windows because drivers, basilar programs, flash, codecs are installed with OS. Obviously you need to learn new stuff about your distribution but you can't expect from a pear to be an orange.
The principal issue of Linux is that now there isn't a good support for blu-ray, 3D and HD audio.
But if we search the near future we can see:
-HD audio support will come with new Pulse-Audio (because all the other components FFmpeg, XBMC and ALSA can support it). (if you use a bleeding-edge configuration this is not anymore a problem)
-Blu-ray are now supported in real time by means of makemkv but this support lacks menus and other stuff that will be integrated in the future with
NFS streaming.
After this consideration I want to point out the cost of the software in the 2 cases:
WINDOWS:
OS OEM DVD 75€
Blu ray software 100€
LINUX:
OS 0€
Blu ray software (makemkv) 0€ (Will be 60€)
So it is true that a Linux configuration now is more limited but there is 175€ of difference that is intended to increase every year when you update the OS 33€/y (if you consider that a new windows OS is relesed every 3y and it costs 100€ to update the OEM license) and the BR-player 60€/y.
This difference is 1/3 of the total cost of an HTPC system and if you don't waste 93€/y in updating you can buy 8-10 blu-rays. Or better you can donate a part of this money to open-source projects that let you to build a very good HTPC (I mean XBMC, FFmpeg, Pulse-Audio, Your linux distribution and so on).
If you crack your winOS / BR-program this speech has no sense.
In third analysis the maintenance of a working linux distribution is simpler than a windows configuration. I'll explene better reporting my example.
I have a dual boot configuration ( Vista + Ubuntu ).
I use Windows only for blu-ray but when I start windows I had to update the Anti-Virus, Java, The blu ray Player, The Adobe programs (flash), The operating system to avoid some interruption during the vision of the blu ray or only to be allowed to see dthe film (Br-player). Don't tell me to disable the auto update because I did but sometimes messages of updating come out. And a Windows configuration used for all media needs more updating for every damned program. A linux distribution has only one and central update manager that can be sheduled or disabled and let you update programs/codecs/drivers.
In the end if you like Windows use it but don't demonize linux only because you don't want to learn new things or because you don't have a compatible hardware (it's like you want to install an Apple OS on a non apple hardware).
See you soon