Selling upgrades to people buying new construction is what I've done for nearly ten years, and here's the best advice I can give you:
1. Make sure the "bones" of the house are upgraded:
a. Cabinetry in kitchen (42", or tallest you can afford)
b. Wood floors throughout the first floor (keep the flooring consistant, so that if you get wood flooring, get it installed throughout. If you get tile, do the same. Don't get tile in one area, wood in another and then carpet in yet another area. It chops up the "flow" of the first floor.
c. Get fireplaces and any major plumbing and electric, such as double sinks, island in the kitchen, hi-hats.
d. If you're being offered upgrades such as higher ceilings , upgrade them (in the main areas only!) This is a sore spot for me, as I believe that these types of structural items should be included. It's just another way for the builder to get more money out of the buyer!
In any case, these are the things you will probably not tackle by yourself after you've purchased the home.
2. Items that can be changed later (or what I call "bells and whistles"):
a. Counter tops: Formica is fine, in upgraded colors. NEVER get light Formica without a beveled edge, as it will show an ugly dark line on the edges. Stick with dark Formica. Granite and any other solid surfacing is always less expensive done on your own, as builders mark these items up BIG TIME!
b. Appliances. Get the standard stuff and upgrade yourself later. You have more bargaining power at an appliance store when you're buying five appliances, than if you would buying them from a builder. I worked for a builder not too long ago, who marked up appliances to 75% more than what the retail appliances stores were selling them for!
c. Carpeting: get the upgraded padding, if available, then you don't neccesarily need the upper-level upgraded carpeting. NEVER get builder's grade carpeting! You'll be replacing it in a matter of 18 months, especially if you have pets and children.
d. If the builder offers upgrades in plumbing fixtures and lighting fixtures, only consider them in the foyer, kitchen, powder baths and master bath. Stay standard in all other areas, as you can upgrade them yourself later on.
Good Luck!
Hope this helps.