We just had our house built three years ago. Since this is Tokyo, it’s tiny and we had to fight for every inch (OK, centimeter) of storage and making dead space usable.
Take a voice recorder along to the meetings and then write memos afterward. Share the memos with the contractor so that you have written notes of their comments, “Sure, we can do that for free.” before the estimate is written. Make sure to clarify what is extra costs and what is not.
As others say, put LAN cabling everywhere. Make sure to use high quality cable since bandwidth needs will increase as time goes on.
I ran the wiring for a home theater system with HDMI cable to where the projector goes. Put a conduit there for future proofing, as cable requirements will change. We had conduit run between rooms as well, but most people don’t go that far.
Full blown home automation systems are beyond the scope of most people, but they are getting cheaper. You can look into a simple system. I’d look into outdoor network camera, but that’s just me.
We put ceiling speakers in our house, but that’s overkill for most people.
On a more practical level, but fourplex outlets where there is high electrical usage. We put two fourplex outlets in our entertainment center and that wasn’t enough.
Since rooms get rearranged, couches moved, bookshelves added, etc., add more outlets everywhere.
We spent a lot of time looking at natural lighting, which gives our house a more open look. A lot of people have commented on it.
We hired another architect to check the drawings and do an inspection, and he caught a major problem.
We also spent a lot of time going over the kitchen. Unfortunately, because of size considerations, we couldn’t get a lot of what I’d like, it still made it much nicer than what was suggested.
A few things to consider: will both of you be doing cooking at the same time? Plan that into the flow. Also plan for heavy use, Thanksgiving or Chinese New Year, when there will be many cooks in the kitchen.
We looked into an inline hot water heater by the range to get really hot water for boiling. Lacking the space, we didn’t do it, but I’d look into that for the States.
Think about light switches carefully, where it’s nice to have two-way switches and such. Think of how you will be turning them off at night, so you don’t have to walk through a dark room to get to your bedroom.
Extra space in the entrance closet for coats, etc.
Look into the house design from a standpoint of passive solar heating.
I think they are getting more common (standard?), but attic fans are good.
I may think of more later.