I'm building mine out right now and I am for the most part a novice builder. I don't have any regulations to deal with so that's probably different than most situations. Anyway, this is what I have learned so far:
1. You will basically be building on a slab so take extra time to ensure you have everything planned out before the concrete is poured.
2. Attaching the structure to the frame is easy but filling in the space where the frame and interior walls meet is a pain. I'm taking extra precautions to ensure I get a tight seal on the living area.
3. I already know I have and will continue to have a mouse, bug, and dust issue and am planning to use closed cell foam on the living space to help combat these.
4. Make it as tall as you can afford. I went with 16' side walls and I would say that's the minimum if you want a usable mezzanine.
5. Pay to have a ceiling put in when the shop is built. I did and we really like it.