Hey James...
The first floor will remain concrete since it is planned as a garage and workshop. We will pretty up the shop area with an epoxy paint or something similar. The jury is still out on the garage floor; TBD.
The second floor is all living space, and that is where most of my attention (and whatever remaining budget) is focused. You and I PM'd this subject a bit when you were building your castle, so you already know that I am a Woodie. Wherever possible, I prefer the real McCoy. I am right now in the midst of laying in some 800 sq ft of prefinished natural Ash Bellawood hardwood flooring at our primary residence. It is absolutely gorgeous, and at $3 per sq ft, is pretty hard to say "no" to. In my heart of hearts, I would love to have something similar in my pond garage/apt. To tell ya the truth, my ultimate goal would likely be natural hickory. Whoa!