eddie- alot of what you have said is so true. All good points, and great ideas.
I want to add two more things. zoned HVAC and sun location.
HVAC-Depending on type of house you build, zoning is a wonderful thing. take my house for example. Its a raised ranch with huge 6 by 10 windows facing south upstairs in living room. In winter, its gets warmer in living room then bedroom on west and north side. zoned heating balances out the comfort resulting in heat savings. for AC, the lower level is always colder even with vents closed when ac is on then upstairs, but with zoned AC the first floor is balanced out compared to upstairs resulting less AC run time.
Sun location. When I moved here, my garage doors faced the south and had no windows. I had to use the light everytime I went in there during day. I replaced it with simple windows last month and I am marveling on how much light I have now and I can see without turning on the lights when I need something. Remember I mentioned my huge windows in living room?, it too faced south so its gets warmer in summer/winter when sun is out, and chilly when cloudy in winter.
As eddie mentioned, you need to think through on how you WILL, not want using the house features/layout. think where is garage/front door is located. N,S,E,W? same with rest of house.