For me, my early fortress design depends on whether or not my "real" fortress will have a grand entrance. That is, a multi-z-level entrance complete with engraved columns and vaulted ceilings and waterworks, etc. If I am putting a lot of thought into the entrance, I tend to build a fairly self-sufficient minifort off to the side on the surface.
Key attributes for this mini-fortress include 50+ modest rooms, nice dining / praying / socializing facilities, plenty of storage for the random junk needed in constructing the real fortress, a barracks and weaponsmith, exploratory shafts dug to find the caverns, fairly robust food growing / processing, and easily-expandable and repeatable room design.
By keeping these miniforts similar to one another, I can set them up in only a few seasons and get right to work on my grand entrance without unnecessary distraction. Because I know the cavern layout I can usually plan some cool rooms that overlook a cavern lake, or rooms centered in the flux stone layers, or interesting ramps that lead to interesting places.
When the real fort is livable, I tend to move everyone except the military out. The minifort becomes a robust surface barracks at that point. You could also turn it into the visitor center, with libraries and temples. Or wall it off and forget about it.
My best advice is to never become too attached to any one part of your fortress. It can really hamper the fun when you're getting all anxious about perfecting this room or that entrance or what have you. A more easygoing design lets you focus on the amazing generated stories.