If you delay the closing date, you may be responsible for the insurance for the house plus the interest of the fund the builder borrowed to build your house.
For upgrades, hardwood floor is almost a must because it'll affect the resale value. Pot lights are also considered good investment because it's something you can't really do after the drywall is put on. Use ceramic tiles for foyer, kitchen and bathrooms if possible. Any energy efficient feature is good because it'll save your energy bill.