It seems ground-sourced is a much better idea than air-sourced, and it seems to me you could install the ground loop with/under/around the foundations for new builds.
As far as indoor distribution goes, it seems like a low-temperature hydronic system would be most efficient, and most comfortable. Or at least a hydronic (instead of refrigerant) loop to multiple chiller/heater units, which would be easier to install and change.
You're right that ground-sourced should have better efficiency and thus running costs, especially in winter.
The gotchas are the energy used to run the circulator for the ground loop, and the fact that over the course of a heating or cooling season the ground temperature lowers or raises, respectively, by enough that the COP isn't even much greater than an air-source system (but this would definitely vary by climate).
Coupled with the much higher installation cost, it's a bit hard to make a system pencil out for a building the size of a single-family house.