I'm not directly involved in buildings, just construction observation from the client's side. Obviously, I deal more with condos and co-ops than free-standing houses, but I've seen so many people who buy $2M apartments that become serious money traps because they were developed by fly-by-night building companies:
- Have an independent inspector go through the building. The builder will want to provide their "own," but pick someone you're comfortable with.
Make sure that the roof is watertight. Make sure that the contractor is willing to have a 20-year No Dollar Limit warranty on the roof.
Make sure that the windows, doors, and skylights are properly caulked, are installed properly, and have 5 to 10-year warranties and acceptable Energy Star ratings.
How are the walls? Gypsum board is what's common, but a bad leak (see above) can require an entire re-plastering of the affected room.
Have your own architect and engineer review the plans. The builders work for themselves, but the architect/engineer work for you. You'll want the house to keep you cool in the summer, warm in the winter, and dry year-round.
Good luck!