Multiple conduits to the street, to make it easy to pull new communication utilities if they arrive, assuming utilities are undergrounded from the street to the demarc. If you've got a gate, two cat6 runs so you can easily do phone and ethernet to the gate controller.
Well labeled electrical circuits. Maybe a panel setup for load shedding non-critical loads when on generator/battery, but maybe just a big generator. Or maybe build somewhere with reliable utility power.
Air exchangers (HRV/ERV depending on climate) on multiple sides of the building with temp/humidity sensors so one can pull in cooler or warmer outside air. Separate air handlers per floor. Reasonable access to the attic(s) to replace equipment in the attic and for inspection of attic and under roof conditions.
Maaaaaybe wired sensors so the thermostat knows when a window is open or for a security system if you're interested in that.
And a deck or widow's walk on the top for stargazing (with a vibration-isolated telescope mount, if such a thing is feasible).
In my part of the world people tend to build large houses on small blocks of land, leaving very little space for a garden (which is doubly stupid because the climate is so pleasant most of the year); I would do the opposite, and build a small, compact house to maximise the outdoor space.
I would also have a closet somewhere in the house big enough for a 42u rack, with a 220v 30a circuit, and some cooling.
The other thing I would do is have all the switch boxes be extra depth so that smart switches and dimmers will fit in better. It is hard to get them into standard depth boxes.
1. DOCUMENTATION!!!!. Pictures of every wall just before drywall goes up. Pictures of the yard showing plumbing locations (incoming, sewer, sprinkler, etc). Electric circuits diagrammed and clearly labelled. Smart home software documented as well. In 5 years, you won't remember how you set up that docker container!
2. Smart home with everything self-hosted. Zigbee (my personal preference.. I have 50 switches) or Zwave devices. Nothing that can phone home. If it makes me download an app, then I don't buy it. Don't use a RPi... I've had them die too often. You want something that will still be working in 10 years, and can be sold with the house if need be. Also, everything should fail "dumb", meaning that if the smart home is inaccessible, then a switch still works as a switch.
3. Security system (cameras, sensors) that is also completely self-hosted, wired, and can integrate with smart home software. NVM, POE cameras, etc. If I have to change batteries, then it's a no-go. Interior motion sensors. Window/door sensors.
4. Automatic closet lights. My current house had them when I moved in, and they are awesome. Not tied to the smart home at all, just a switch on the inside of the door jamb.
5. Whole-house, multi-zone audio, integrated with smart home. Imagine audio following you as you move through the house!
6. Cat6 in all rooms.
7. Well-ventilated, secure server closet. If someone breaks in, I don't want them to be able to destroy the hard drives with the video evidence. I also don't want it to overheat.
8. Electrical panel monitoring on every circuit. Information logged to the smart home, of course.
9. Fiber internet if available. I love it!
10. On-demand water heaters are nice.
11. Permanently (and discreetly) installed Christmas lights. Again, I'm going to go the self-hosted route for the software. It's much easier to route power if planned for ahead of time.
12. Thermostat connected to smart home. I use a Zigbee one. They are harder to find, but I love it!
13. Dumb TV. I don't trust anything that wants to connect to the internet... especially not a TV! lol
14. Ceiling up-lighting. Mine is tastefully hidden behind crown molding, but it is a nice effect. It can come on automatically when you enter a room at night. You can also use colors for different notifications, such as someone at the front door.
15. NO fancy doorbell. Again, I don't trust any of the current companies (Ring, Nest, etc). I have my self-hosted cameras (Reolink RLC-811A) that have on-camera person detection and I integrate it with my home automation.
16. Outside lighting. Mine is automated, of course. It looks amazing and is much more secure than just darkness everywhere.
17. Buried electric cable. Again, my current house has it. Neither of my neighbors do, and both have had tree limbs knock out their power.
18. Insulation. I'll say it again: Insulation!!!! Do more than required. It will save you money because electricity will just get more expensive.
19. Solar? I'm undecided on this. If I do get them, I will buy them outright.
20. Whole-house water filter.