I am building a house right now and I can tell you it will end up costing me at least 30% more than an existing house of similar size. The reasons are
a) Houses are cheap as hell right now and people are willing to take a bath to get rid of one when they need to and
b) "getting exactly what you want" almost always means getting a more expensive option than those chosen by developers/speculative builders. This becomes more and more apparent to me every day, and is especially true since this is my "lifetime" house and resale value is only a minor concern for me. You end up erring on the side of durability/longevity/energy efficiency instead of economy. I have chosen that and it is OK with me because I can afford to make these decisions, and end up with exactly everything that I want.
If you cant, or if you intend to sell within 10 years, I would buy a house and not build.
eta: I looked at about 60 houses in my area over an 18 month period and it became clear to me that I would never be satisfied with any of them, so I have no regrets about spending more
This post was edited on 11/7 at 7:30 pm