I have built several homes and we have learned to skip the fireplace unless it's a real wood fireplace, and skip the large soaker tub.
Upgrade the windows, kitchen counters and install a whole house backup generator. I always double check the views of the windows too before they cut them out. Why look at the corner of your neighbors house for 10 years when you could move the window three feet and have a view of the trees? Also, make sure builder installs double hung windows with low-e and argon.