Another vote for a few here:
Radiant floor heat....had this in a barn conversion we lived in in the UK. Timer came on an hour before we woke up and it was BRILLIANT to have.
Oversize (height and depth) on the garage. Also decide if you are going to have one be a dedicated shop or not. Floors drains are another must have along with a full bathroom with large shower. Also like the idea of meat processing and a walk in cooler.
Higher ceiling heights all the way around. Open and airy.
Natural gas to the decks and patios. We had this when I was a kid and it was great to never have to worry if the bottle was going to run out.
Here a couple of particular interest to me:
Upgraded electrical service. It was mentioned a bit above but this is big to me. Think about at least twice what you thing you may "need" including 220 outlets in the shop area.
When designing the kitchen, if it is important to you, I would design around the appliances I wanted. I am a semi-professional cook and kitchens either make me smile or piss me off

Plenty of storage, real pantry, outlets, venting, lighting and the oversized workspace mentioned above.
Finally, and this will be VERY high on my next place, a sauna. Totally personal but not only do I feel much better when I sauna regularly but I believe it promotes health. You can go from a small infrared unit in the house somewhere to a stand alone wood-fired unit ....along with all kinds of cool add-ons for lighting, sound etc.
Good luck