Not only can you buy the perfect plot of ground on which to build your home, but you can position it on the property to take the best advantage of the view, or solar effects if you're going green. You may be limited to some extent by set-backs from the perimeter of the property, but you get to build the house you want, with the exterior finish you're looking for, and are not bound by homeowner's association restrictions, in most cases.
Since you are choosing everything, from light fixtures to flooring, you probably upgrade these personal touches. Anything in the home that is above standard makes it more appealing to a potential buyer. The design of the home will be unlike any others, and will be worth more than a standard cookie-cutter home.
Since you're building from scratch, you can install energy-efficient appliances and units, and start with higher R-value insulation, rather than try to retrofit an existing structure. You can also position the house on the property to take the best advantage of the breeze, or to maximize solar heating.
If any member of the family has allergies, you can control all the materials used in the home, to cut down on reactions.
Since your home is new, repairs and maintenance are at a minimum for the first five or so years, so the money you would normally spend to maintain an older home can go into upgrades within the home.