OK, everyone seems to ask the same questions when walking through our house:

Is it how you imagined? Were you on budget? Would you change anything?

And we say YES to all of those. Nothing is ever perfect -- live in it, evaluate it, and think about how to make it better for next time.

Here are some things to consider and others we will change when we do it again:

Even if you can't afford radiant floors, do a short run for bathroom floors if possible. Forced-air works for keeping the air warm, but tile floors without radiant heat are not comfortable to the bare feet during the winter.
Install a drain in your laundry room. We always had plans to have one, but somehow it didn't stay on our plumbing priority list. It only took one laundry sink overflowing to recognize the importance of having one. Just a few gallons of water on the floor can cause a lot more damage than you might think.
When detailing floors at indoor-outdoor areas, provide durable and weather resistant materials at operable openings. I'm envisioning some sort of strip that catches dirt/dampness between the threshold and where the wood flooring starts.
Beyond just thinking about shades, actually pick a brand that you can afford and detail the head/jamb returns to accommodate them. (We talked about creating an actual recess, but the amount of gymnastics to achieve this was beyond our budget.)
If you are planning on having pets (cats) plan for them and their litter boxes. We promised our kids that we'd get kittens when we moved to the new house. Don't ever make promises like that and if you do, be sure to figure out a way to accommodate their litter boxes. When you have an open floor plan it is difficult to confine odors unless you are diligent about cleaning.
On tight urban lots, what is more important: More square footage on the main level, or an attached garage? We went back and forth on this and went with a detached garage so we could have a bigger main level (this is controlled by Denver Zoning requirements). It's more of a lifestyle question, but one that has a big impact on the overall layout and access to spaces in the off-seasons.
Evaluating products for green, quality and cost is VERY challenging. Decide early on what your priorities are and what your budget is. Figure out what you are not going to budge on (but allow room for flexibility :-). If you are trying to build entirely green and use the most energy efficient systems and the greenest products you will be very challenged to do so unless you have the ability to pay for it. In most cases, we tried to select green products/systems but we had to make numerous compromises because of our budgetary constraints. Ultimately, we decided on SIPS and great windows and compromised on items like radiant floors, and planned future installation on items like solar panels.