If your intent is to live in it, I would say go with whatever you may want in a home
More specifically - through the builder, you want to get anything that's in the walls (insulation, in-ceiling speakers, etc) or electrical (recessed lights). If you want to upgrade countertops, I'd probably go through the builder for that, too.
A lot of people recommend upgrading flooring, paint, etc outside of the builder, as you can likely get a better price through an outside contractor for it.