You may find your home automation system will actually use many arduino boards for different purposes.
What I would do if I were you in at this point in get any arduino with a USB connection and start playing with the various modules you will want in your home automation system. For example, you may want to open / close blinds and/or interface with lighting systems, etc. I would work each of these individually. Once you are up to speed and have a couple of "modules" created it will be much more clear how your final system will look and work.
Some notes from someone who has created quite a few home automation systems.
- Some items may be better served using off the shelf products while other parts of your system will be DIY friendly. Arduino is great, but don't get caught by the hammer/nail syndrome (once you have a hammer, everything looks like a nail).
- You may also consider thin clients in your scheme. They are quiet, low power and can do lots of the heavy lifting without a need for a full fledge / loud / high support computer.
- You may find that creating "web enabled" components using an ethernet shield allows for easy integration and provides the distance needed for full house communication.
Sounds like you have the right plan to start now for a house you plan to build in a couple of years. This gives you plenty of time to work out the details, so you know what to wire up when the time comes.