Maybe some of these have been touched on but here are my thoughts based on experience with a purchased home and what my parents did when they built about 12 years ago.
When my parents built their house they put in a central vacuum system. Base unit is in a closet in the garage. The suction power those have is incredible. Something to consider. Not too expensive to install, especially in new construction. Do need to store the hose and accessories which can be bulky.
If I were to build a house, I would 100% not dig a basement. I have had nothing but problems with water seaping through the foundation with heavy rains. In my brothers new house the solder to the hose spigot failed and water leaked into his finished basement. For storm shelter have a closet or shower poured from concrete when they do your founation.
If you have the resources home theaters are fun. Can have a drop down screen installed to come out of the ceiling.
Heated floors are wonderful especially in the bathroom.
Simple roof too. The more transitions on a roof the more places water has to find a way in. Might not be an issue right away but down the road issues are more likely to arise. Also if you ever need to reshingle your home, the roofers will appreciate this.
Run a gas line to your porch if you have a gas grill. Its nice to not have to replace/refill small tanks.
I like the light switch by the bed idea but this also virtually eliminates the ability to rearrange your bedroom furniture if that is something you do.
My parents ran electrical wire under the floor in the living room. Haven't installed any outlets, but that option is there if they ever decide to. Now that furniture has USB ports in them and electric reclining, it would be nice to be able to plug these things in directly underneath them. Especially if its in the middle of a room.
we have a floor outlet in our living room, that is really nice. Hidden under the couch. Does semi-limit furniture arrangements but the place we have it is basically guaranteed to have a couch over it.