As someone who went through some years of architecture undergrad before changing majors, plus watched my dad draft changes to my childhood built home, a few notes.

1) Time costs money. Building time, change time. Custom increases build time, and plan changes increase engineer / architect time to recertify.

Consequently, I would highly recommend starting from a base plan!! (The first exclamation mark I used to register serious recommendation; the second to indicate emphasis.) These plans can be purchased from many sellers, and are already code-compliant.

Thus, your problem space can be windowed down to "What do I want to change from the pre-approved plans?" + "What needs be done to realize those changes?" With the remainder of the house being "as is" and requiring minimal plan work.

This also avoids things becoming overwhelming, as the building starts "done." And should stay "done" (except for the part you're adjusting currently).

1b) Change expense is highly variable, because you're changing an approved system. Sometimes a wall movement will be no charge. Sometimes same will require a new microlam beam and redesigned joist system to realize.

2) Homes are personal. Architects design homes for a variety of reasons, some of which may overlap your personal needs. Think about how you will live in and use the space (as in, on an average Tuesday), and design for that. Assume you will not completely change your lifestyle just because of a new house. ;)

3) The wedding choice problem (from catering experience): anything can be changed. To meet your financial and time goals, only some things should be changed. Come up with some ruthless method of deciding which things are in which category. Expected enjoyment must be > change cost.

4) Work from major to minor changes. Structural changes -> orientation changes -> internal system changes. The former can impact the latter, resulting in cascades of changes. The latter rarely impact the former.

5) Do everything and anything you want in-wall that would make your life easier (insulation, conduit). This is trivial during construction when walls are open, and a pain in the ass after everything is sheetrocked.

6) Look at products like an engineer. Cost difference vs return (financial of according to your value metrics). Manufacturers have incentive to sell you everything under the sun; only some things make sense.

Most things don't make sense. Make something prove itself, rather than starting from an assumption of change.

7) Find a quality builder and monitor them. Show up on site, know your plans, and check random things. Some builders will cut corners; they will cut fewer corners if they know you're watching. F.ex. don't let them bury construction debris in the foundation trench (will eventually settle).

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A hodgepodge of things I've realized are important: foundation[!!!] (basically can't be changed after house is built, easy to plus-size/prepare if in an area with concerns), insulation (if hot or cold climate), foundation drainage (if rainy climate: it's trivial to bury a proper PVC french drain+gravel or gutter drain during construction, and a pain[!!!] after), conduit (home runs to central data closet), joists sizing / stiffness (if you'll be there a long time, don't minimally-size floor joists, as they will weaken over time and lead to bouncy floors).

Misc ideas: geothermal heating and cooling (if geology and temperature support), hybrid hot water heater (heat pump), natural gas heat appliances (incredibly cheap in terms of fuel)