• 3 car garage
• 9' basement
• Separate basement entrance if there's any chance of ADU (and definitely do it if the slope of the lot means the basement is practically up against the land anyway; if that's the case, it's likely only $1k or so to make that change)
• Dedicated electrical outlet in the garage (that's on its own breaker), and might as well add a 220V outlet there too
• Exit door/man door in the garage
• CAT6 ethernet cables throughout the house
• Consider having the builder finish the basement (if they'll do it how you want)
• Extra insulation (depending on where you live)
• Improved flooring (carpet, carpet pad, LVP, etc.) and cabinets
• Fireplace, if you want one

Most of the things above are mostly structural changes or things that are much more expensive to change later.

Here are some upgrades I would do that-- at least more so than the ones above-- have to do with preference:

• railings rather than half walls at stairs
• LVP (or similar) rather than carpet for hallways and most places that are not bedroom (or equivalent, like a den/office/living room), except maybe the familiy room portion of a large open kitchen/nook/family room space, if it's big enough
• walk-in shower instead of a separate bath and shower in the master bathroom (as long as there is another bathrooom in the house that has a tub, or unless you or your spouse take baths somewhat frequently)
• LVP (or similar) rather than tile (tile is hard and cold, and usually more expensive to install, and doesn't really look much better)
• Quartz countertops rather than granite

People are more likely to disagree with this second list, as it has more to do with preference, but I still think most would agree with most of them anyway.