This is exactly what I found after getting a few quotes to replace my current system. And that's heating with propane, which is close in cost to literally burning cash for heat. Payback from propane to geo was 18+ years with a life expectancy of the unit of 20 years (after factoring in the tax rebate.) I am considering building a new and smaller house, and would get another quote, but I'd likely end up with a heat pump with propane. Natural gas is rather hard to get out where I live and/or would live.
Affecting to the cost is how you do the ground loop. Where I live they'd have to drill wells, which is expensive. In other places you can just scrape off the top 10' of soil, run a loop horizontally, and cover it back up. This assumes you have a lot of land that will be grass, not trees with invasive roots.
For a new house, I'd likely just super-insulate the place with an air-to-air heat exchanger to keep the air fresh. R-21 minimum or even higher for the walls, and R-60 or better for the ceiling. I'd then put sheeting over top that to keep dust down and allow for easy access and/or storage. I'm temped to have concrete exterior walls (or brick) for the thermal mass and noise reduction.
I like poured 9' foundations for future basement finishing with a very good water proofing system.
Solar would be nice, but a generator and transfer switch would likely be a must given the area's frequent storms. Some sort of UPS for critical electronic systems, too (alarm, security, phone. You can get older, larger commercial ones on eBay relatively cheaply. Batteries are expensive, though.) Definitely do a whole house surge suppression system. They are cheap and can save you lots of money later. You can almost never have too many circuit breaker spaces in your panels. I have two 200 amp panels and they are 3/4 full. Modern codes require dedicated circuits for many things, and I'd expand on that. A 15 amp breaker is dirty cheap.
I have dual cat-6 runs to each bedroom and most other rooms, and I'd probably expand that to 3 or 4 in new construction. A coax run is useful (all home run.) Pre-wire for speakers in areas you'd want an entertainment system. Conduit is nice for the cat-6 / RG6 stuff. I'd run a 3" PVC pipe from the basement to the attic, but not on an outside wall. You never know what you'd want to run there. I'd also plan for PoE networking for surveillance cameras looking at all entrances, in the garage, and places like the family room and kitchen.
Obvious things like very low-E windows, make sure you insulate the corners of the house (most builders don't!). I'd also write in the contract that I'd have the exterior assessed with an infra-red camera during winter for any heat leaks and require them to be fixed (within limits, of course.) One missed wall bay or something can seriously kill efficiency. My current house has a vent pipe in an exterior wall. That bay in the wall gets down to 45 degrees F in the winter! I'm guessing it's to provide air to the water heater, but I'd likely go tankless. Definitely nothing that uses air from inside the house for combustion.
Music to the rooms and/or intercoms can be nice, depending on home size. I'd likely opt for something PoE for the intercom, if possible.
Lots of exterior lights (don't forget switch outlets in the eaves if you like Christmas lights.) For lighting inside, LED strips are very neat (get high CRI ones.) Perhaps in hallways LED strips would be nice.
Easy access to plumbing fixtures for future replacement and upgrades. (It's amazing that builders don't do that now.) For outside, a number of waterproof electrical outlet boxes (we never seem have one where we want one) and several water bibs so you don't have to run 200' of hose every time you want to water something.
I'm sure there's more to be added...