You have just described almost exactly the house I am in the process of building. KNX going in for Heating and Lighting control, (I used Gira mainly from the nice chaps at KNXshop). LinuxMCE, (or similar), in many rooms, speakers in a few others. Not chosen the alarm yet but the Comfort is top of the list. The builders are in at the moment, I have the KNX devices on site and the 1st fix cable is being run when they get back from the Xmas break. Pretty much everything else in your description was so scarilly close I had to check I hadn't written the post myself and forgotten
I was drawn to Pluto Home for the KNX support and have been following LinuxMCE. Not everyone understands the popularity of KNX in Europe, particularly Germany and the Netherlands. In the UK they mainly use it for larger projects, (terminal 5 and Canary Wharf tube stations for example), but that has been changing a lot lately. There are a few posts from others having some frustrations with it and a few people talking about contributing more capability, this seems like the best thread http://forum.linuxmce.org/index.php?topic=5648.0
Vista Media Centre has better integration with mControl and Exdomus Pro and those new media extenders are a great silent solution for HD playback in your lounge & dining room, but if you were willing to put up with the pain and strife on Vista Media Centre you probably wouldn't be the kind of person on these forums, (my dirty secret is I am sometimes tempted). If you want to contribute any KNX code to match VMC capabilities, all the better, I guess you will have some grateful users. I'm in a kind of limbo state with my implementation until I can gain enough skills to make this work or find an alternative, (nothing yet has LinuxMCE's flexibility, but then I'm stuck without KNX)
The current range of Atom platforms, like the EEE are not really powerful enough for all HD content as the Intel Chipset isn't up to much. You'll probably be OK with 720p, (which is pretty good), but those big HD downloads will stutter. If you could hold off into the New year for the Atom based platforms with the Nvidia 9400M graphics you will be in a better position, (supported with the latest Beta Nvidia drivers). Particularly if you want audio on your HDMI cable. If you want to do that today you would need a Core 2 Nvidia system, (perhaps look at a Mini-ITX based one), and if you want that to be silent you are looking at HushPC and the like, which is big bucks. Or if it is not too late, you can get HDMI Euro face plates and stick the PC's in the loft.
Touch screen drivers seem to be available for most devices, but UI2 is not considered a great fit for touch screens. UI1 works great, but is not as pretty. It is particularly good when the touch screen orbiter is actually just controlling another MD.
You can have your tuners in your Core or MD's or both for MythTV which works great in the UK, (been using if for 5 years). Not sure of the advantages of VDR as I have not used it, but someone else has said tuners need to be in the core.
LinuxMCE completely uses external storage. I built my core a while ago and all my storage is connected to it via SATA, but I would probably have used NAS devices if I did it today
Keep in touch with the forum and let us know how you get on, (or get in touch directly). Looks like you are going to be a few months ahead of my build and going through the issues I will before me so I'd be happy to help.
Couple of questions,
Did you go with DALI for your lights, (with one of the KNX-DALI gateways)?
Did you pay for the full version of ETS, or stick to the ETS Basic devices?
Have you looked at HomeServer from Gira?