jokkemokke,
To give you a better recommendation for your new design approach, it could be good to know more about your home automation project. Is it a dedicated Arduino system? I could infer you are using radio controls, an Ethernet shield, sensors, etc. Remember also that you can program your Arduino using Mac or Linux.
tuxduino,
Due could work but still the issue of 3V3 to 5V conversion that would mean extra money.
Finally, I found an interesting book on internet (I haven't read it yet) entitled "Programming Your Home" by Mike Riley that could enlighten you a bit more.
Regards