If you have a basement, make the walls 9 or 10' high, not the standard 8 ft., that extra headroom is great. Cost me less than $1K more, and I can put an 8' ceiling under my ductwork and beams.
Exterior 2x6 walls, that's one I regret not doing.
Plan elevation with gravity drain for basement bathroom.
Two electrical panels up front. It's amazing how fast you run out of breaker spaces.
If septic tank, oversize it. I oversized mine to allow one more bedroom, cost of the tank was $50 more.
Ceiling fans in all rooms.
Plan all furniture locations and plan outlets accordingly. Go with extra outlets than the minimum required.
Wide stairs, I put 4' wide to my upstairs to make it easy to carry furniture up.
3' doors inside, as others have said.