I'm in a similar situation as you, building a house and trying to put together home automation plans just before the electrician starts wiring. My current plan is certainly to still have the house "work" if all the HA stuff seizes up during Y3K or some other disaster. As far as keypads, I'm planning on using a couple in the house (front door & garage), and will fit them to switches that are wired to switch a light. So rather than having the electrician wire a generic unused box as a switch, he'll do the normal "wire a foyer switch to a chandelier" at the door. Once replaced with a KPL, the KPL can still be used to switch on/off the chandelier, as well as controlling that light via the ISY for day/night or other uses. I can then use the other KPL buttons for other scenes and such. I am minimizing as much as possible the "8 light switches in a row) syndrome (for example I may eliminate some switches direct wired to electrical outlets in favor of doing that via HA later if desired), while still retaining normal usability, and am happy not to have anything even close to that!
The vast majority of my automation wish-list will be accomplished with no extra wiring from the electrician, though I will have him install a bridge in the electrical panel and a whole house surge protector.
There are some other items on the more esoteric HA list, mostly dealing with low voltage powered things, but I'm hopeful most of them can travel via RF (thermostats, sprinklers, contact switches on doors, etc). I currently am not planning on using inline-linc type devices to control some of the unsupported things like radiant floor heating, because it seems like pushing my luck.
Good luck with your project! Keep in mind this stuff is designed to be retrofitted into existing homes, not to have homes built around it.
Dave