What are things you would of done different or would do again. Leaning towards a barndominium type house with a basement. I live in Central NY.
Ive only been in mine for about 8 months, so my thoughts aren't informed by the years... but I did put countless hundreds of hours into the effort, and think it turned out ok. Lots of good advice here.
1.) If you are going to come back to it every day for decades, you want it to be a good looking house. That varies by person, but for me it was modest and simple lines that I thought would age well. I tried to (hopefully) avoid things that would "date" it excessively in 30-40 years. Although I looked a dozens of building styles, the barndo's didn't make the final cut, as I decided I didn't want to come home to a metal box at the end of the day. YMMV obviously depending on what you value.
2.) Along those lines, my own initial designs were still a little TOO boxy and simple, and we eventually realized it would short us on windows. By adding a few bumps and corners, it increased the wall area enough to add windows into offices, baths, family room's etc. Some advice from an architect friend really helped us out here and the house is more pleasant with the additional daylight into smaller rooms.
3.) Open floor plans are nice (and trendy), but if you still have kids in the house, then there is such a thing as TOO open. Sometimes you need them around the corner and in another room! Also, big living rooms a can be challenging to furnish, as the "groupings" of furniture don't work out well. The major floor plan change we would have made would have been to actually shrink that area and make it a little cozier. The only dead space in the house is in the living room.
4.) As mentioned several times, when it comes to contractors, cheap is.... cheap. A quality sub will do the job once, and usually save you money in the long run. In my case, what it really bought me was speed. I was able to finish my house in ~5 months, and that saved a fortune in rental and financing costs compared to the more common 12+ months that most houses were being finished in at the time.
5.) This was mentioned above, but you don't have to make it fully ADA accessible right now, but consider it in the design. For instance, my wife scratched the shower in favor of a large soaking tub, but the space is there to remodel it into a roll in shower some day. If we are still here in 30 years, we can worry about it then.
6.) Lots of closets, big pantry. Storage is a real difference between a tract home and a full custom.
And I guess my last thought. I can't predict the future, but energy has always been a volatile thing in the world, and in NY you will need to heat and cool. Although the numbers may or may not pencil today, it always seems wise to consider energy efficiency into a design that you intend to last. In my mind, it's good to minimize dependence on things you can't control.