I feel like quality, solid, windows and doors have a huge impact on how a house looks and lives. Also, quality hardware is important. I think touching a substantial door knob sends a feeling of permanence when entering a home or room. Oh, and all trim is important but the handrail on a balustrade must be heavy & substantial bc it will be touched constantly.

we spent a lot on upgrades that no one would ever see. best windows and doors we could afford, for low solar heat gain and thermal quality. . extra foam insulation. metal roof, highly reflective.and highly emmisive. appropriate colors. window and glass door placement, vs sun angle.
five years in, life is good.
meet with a leex adbisor, before you get too far into planning. even if you don't choose to follow through the wgole route, as we did, green principles, and leed guidelines, will get you a great house, with reduced power bills, or in our case, plus solar none.

"Best non-cosmetic upgrades" is as subjective as "best cosmetic upgrades."

I had clients who wanted "solid" and got 2"x10" floor framing on 12" centres, but then chose cheaper vinyl windows because of price...and a "window is a window."

BTW, 2"x6" is not necessary to achieve R13 required in the Bay Area, Zone 3.

If you look at the completed projects of architects you're considering you can get a 'feeling' for whether the homes they design will meet your needs. And 2" thick solid wood stile and rail doors on ball bearing hinges can help. Interior too.

ps, I commend you for trying to look ahead, beyond decor. in the long run, its it's the stuff you can't easily see or change that really makes a difference

Yes, my question is - is there anything I should specifically ask the architect to incorporate into the plan that most people don't think/know about? What type of structural improvements really make an improvement?

One thing someone recommended was adding insulation to interior bedroom walls. This will help with soundproofing (especially the master). I would not have known to do this.

Jeremy-

Just be aware that, when you start adding insulation to interior walls, you are creating different zones and isolating them from a heating standpoint. This makes it more difficult to maintain uniform heating temperatures throughout the house. Personally, I wouldn't do it.

Not sure this is considered an upgrade, but I would recommend either attic trusses or stick built roof framing and a steep enough pitch to create useable attic space. So glad we did on our recent new build!

Kathy, I definitely would want to do that but my understanding of the code is that if the ceiling height is more than ~6 feet, it is considered usable space and goes against my allowable square footage.