Whoa, whoa, whoa!
You are building a house and are worried about components?
I would worry about the house wiring first and foremost. If you haven't done that already, and this house is new construction, then I would be sinking $5,000+ to ensure that the ENTIRE house is wired exactly the way I wanted it.
If it is a dedicated theater, with a 12-15' viewing distance, then front projection would be my recommendation.
For the room itself, a bit bigger doesn't hurt at all, but it depends on the real estate that you are able to give up. Likewise, a bit more height in the ceiling is always more visually inviting and provides more opportunities.
All of this just comes down to money of course.
A good surround setup will deliver solid stereo playback. A good front projector will deliver great image quality, but that requires proper lighting and a properly designed room using the right colors and a focus on details.
But, with a whole house going in, I would find a spot to put my electronics for the home and I would wire to that location with everything - phone, internet, cable, audio, video. Dedicate a couple of racks worth of space to the equipment and do it really well. Add some good RF universal remote controls which everyone in the house can use easily and you can have a killer system.