The other things to consider is upgrades that would cost more once the place is done. I know it was debated in the new house thread, but the one thing that comes to mind is bathroom rough in for the basement. Mine cost me more to do by myself than it would have cost to get it professionally done by the builder.
Also running cables (RG6, Cat6 network, etc) is more later on.
The other thing I never thought of until doing my bathroom in the basement, is what kind of tub you want. I say this now because the only time you can get a 1 piece tub in is during the framing stage. If you want a 1 piece for the downstairs bathroom it might be an idea to have one set into your basement.
Unless of course money is no object.
But I still say it's good to get things done that are expensive to upgrade later. Sounds like you and/or the wife want to make the place as nice as possible. Do you have the cupboards you want? What about the carpeting?
There's all sorts of things you can spend on upgrading your new house. Just make sure you spend it wisely. (which it sounds like you are trying to do.)