Congratulations on such an amazing milestone! TheBard and I had our house built about 6 or 7 years ago. The one thing I wish I had done differently was to choose a better quality kitchen floor tile. We opted for the builder's basic vinyl and it ended up discolored and scratched up within a few short years. We just replaced it last month. Get the best quality you can afford because initial installation will be easier and more affordable than future renovation.
The only other thing I can think of is that I was unprepared for the sheer number of details you have to inquire about. During an exhausting session with the builder's rep, she asked if we wanted a fan hook-up in the dining room ceiling. We said no, not thinking that even though we wouldn't have a ceiling fan in the room, we were going to need a light fixture for a chandelier. Because the rep presented it as a "ceiling fan hookup" as opposed to a lighting hook-up, we ended up with a house that's not hard-wired for a dining room light.
I guess the moral of the story is to take your time when you're deciding on your options, and think of every little detail. It's easy to overlook something when you're feeling a bit overwhelmed by the process.
Hope that helps. Best wishes. :)