We custom built maple cabinets throughout our house. Interior doors are all solid pine and fortunately for us the stain matches really good on the pine and the maple. Maple doors would have been twice the cost of pine. Solid interior doors are the shit.
When I built my house I gave it alot of thought in advance since it was custom. I agree with most everything in this thread.
As for exterior insulation we have 2.5 inches of foam and 1 inch of blown cellulite, the highest our electric bill has been for a 2500 sq ft house in the dead of summer has been $161 and that with dual zone AC units running.
A couple of things I haven't seen mentioned are I caulked both the lower base and upper exterior walls before sheet rock went on and added Murphy (hurricane) straps to every rafter that meets the wall headers. Framers only toe-nail rafters to wall headers but I wanted a better mechanical connection. It's going to take a helluva high wind or tornado to lose the roof.
I made every effort to hold my builder accountable for everything. I told him that he was the Manager, Supervisor, and QC inspector I expected him to act that way. But still, he fucked up alot of stuff that had to be either redone or corrected. I ended up suing his ass over some improperly laid bathroom tile he never corrected. I won a judgement against him in small claims court (he didn't bother to show) and promptly placed a lien against his personal house. I got my judgement check in less than one week.