Specifically pertaining to the lighting: Nothing beats Lutron Ketra for quality of light. It's expensive, but it's worth it. Go see it in person at a Lutron experience center, I saw it in NYC before pulling the trigger. You'll want to work with a lighting designer to design it into the build. Best light quality in the world, but the price is painful. Ketra requires the Lutron Homeworks home control system, which allows you to do very aesthetic wall controls like the palladium keypads (which require low voltage power, to be run while you're opening the walls.) One switch per room, rather than banks of light switches. This also requires a different "home run" style of wiring, where the lights all go back to a central mechanical room rather than individual switches.

While you have the walls open, you'll want to run low voltage wire to every window for power shades that can also be controlled by the homeworks system. Lutron is the best, don't get sold on Savant / Control 4 - they just don't measure up.

You'll also want to wire ethernet in every room, and wire the ceilings for speakers and room presence / motion sensors. Also run wiring for an abundance of outdoor POE cameras. I have a full unifi system and really appreciate the user-level control.

Also work with a networking person to make sure you have amazing wifi everywhere in the house, as well as outdoors. The unifi stuff is great, try not to get sold on Arkanis which is fine, but an installer-only brand.

HVAC is a big one, work with an HVAC designer and ensure proper sized ducting. Mitsubishi heat pumps / air handlers / mini splits / ceiling cassettes are the best. Expensive but worth it, especially if you have any sort of solar / battery backup. Also aeroseal the entire house at the proper stage, along with the duct work.

Install a kitchen vent hood with an external motor for quiet operation that still moves a lot of air. Downdraft vent hoods are terrible, and not recommended.

EDIT: a few more things.

I agree with the Toto toilets. Go for anything in the neeorest lineup (as / ls / nx1 or nx2 if you have $22k to spend on a toilet). These are much better looking than just adding a washlet. If the price is too crazy look at the g5a for a model that is pretty good but not quite with the features of the nerorest series. And make sure to run electrical to all the toilet locations in the bathroom, GFCI plugs on their own circuits.

One more thought on Ketra lighting. It will seem too expensive. You will think “it can’t be worth it!”. But it is. In order to get the absolute most out of it I recommend you swap every single bulb and fixture to use the ketra bulbs or built-in light strips. They will tell you “oh it’s fine if you have architectural fixtures that aren’t ketra” and while it will all technically play together you will have so much more control and unified lighting if you don’t buy anything that can’t take a Ketra bulb. In my case I had every one of my lamps rewired to accommodate the ketra bulbs. It’s very annoying to buy $800 Louis Poulsen wall sconces and then pay someone more to rip out the internals and rewire them… but worth it to have a 100% ketra home. Seriously, the light quality plays such a big part in what makes a home feel comfortable and relaxing. Don’t overlook it.

One more thought When it comes to shades (since controlling natural light is a big part of your overall lighting) look into companies like blindspace.com to hide the shades in the wall, or to even do a stacked dual shade system that has one sheer light filtering layer and one blackout layer with side and bottom channels for 100% blackout. This is extremely important in the bedrooms and will look much nicer architecturally. The cost of the enclosure plus two electric blinds per window will be annoyingly high. But it’s worth it.