Just my personal opinion: I would go with the 9 ft ceiling if you can do it.

What size is your new home? I am asking because it might make a difference to go with the expansion to 1300 sf rather than the ceiling, but would need to know that fact first. Also, is the entire neighborhood new or is this infill type construction? You don't want to be the largest house in the neighborhood.

PS - I'm not a designer. I'm a Realtor in an area without basements (S Fl).

Total sqft would be 2916. Standard basement is directly underneath living room and dining room, which spans about 630 sqft. I feel that it was certainly large enough to have a bathroom and either a gameroom or gym. It is probably too small to have a wet bar and media room to be added on. The neighborhood is relatively new with 2/3 of the lots sold.

Are basements typical for the neighborhood? If so, do they take the standard or do the expansion?

If you are building with an eye toward resale in the next 3 to 4 years, its likely (??) the builder will be finished with the entire neighborhood so your competition will be resales in your neighborhood and surrounding area. How does your proposed basement compare?

Edit: Find out from the builder what the projected build out is for the neighborhood. Some of the new construction neighborhoods in my area are huge and are on a 10 year build out period. This would impact your decision because you would be competing with the builder if he is still selling/building in the neighborhood when it is time for you to sell.

An option I'd want is roughed in plumbing for a bathroom, even if I had to finish the bathroom later. I think the egress window would be necessary. FWIW basements are the norm in my neighborhood, and most are finished nicely and have full bathrooms.

Yep I do have rough in for bathroom. I am an out-of-town buyer but based on my limited research, the resell properties seem to have 50% finished and 50% unfinished. Of the unfinished basements, I think there is a 3:1 ratio of full and standard-sized basement respectively.

In a basement, I'd prefer 8 foot ceilings. Plumb for a bath. Unfinished gives the next buyer options. Egress windows, at least two is ideal, but one would be essential.

I'd go for option one: a full basement rather than a partial.

Yes, full basement...

In a basement, I went (and most do around here) for 10 foot ceilings. So obviously 9 ft given your choices. But we don't do 8 ft ceilings for anything in NC. We are tall down here..... From my new construction rental townhouse that cuts serious corners like hollow doors - 9 ft up and down.