If you go with bridges, it may look like this:
3 z-levels above ground, with more traffic on the level above, some traffic on the level below, and some large bridges somewhere about 10 z-levels above (as roofs, so i could make proper rooms). Fooling around with invaders off, so this totally doesn't care about defence.
All the way to the left the access staircase from groundlevel, connecting catwalks stretching past one residential tree in the northwest, the other residence is in the southeast (the main dining "hall" is directly above). The brown =s are a small farm on constructed (wooden) floor. To the far east, the office of the expedition leader.
The fort has a total of 62 beards; most workshops are on open floor, and there are still a few underground constructions (food storage, well, largely unused dormitory). I still haven't found a tree to put the depot in.
Bridges can be built in and above trees without hurting the tree. "Twigs" remain completely un-pathable, bridges don't change that; you need "open space" adjacent to "branches"; build your bridge so that it touches the branches cardinally and covers the open space, that allows your dwarfs to step off the tree (including diagonally). To provide a roof, bridges must be built over open space; if there's any tree feature overlapping the planned bridge, the bridge can be built, but the tiles underneath will still count as "outside". You can "bridge-hop": build a bridge far out into the open, then start a new bridge from the outmost tile. If any part of that new bridge is properly supported (adjacent to branches or trunk) it will not cave in and permits passage; this way, you can cover 20-tile gaps between trees just using a pair of bridges (instead of twenty floor tiles, built sequentially; and you'd need a place to attach floor without making the tree disappear, since floor, other than bridges, cannot co-exist with tree features).
PS: young trees will still grow, and may grow in ways that break bridge pathing. In one fort, i wondered a lot why a bunch of dwarfs got "slept without a proper room" unhappiness while they had very nice rooms - it turned out those had become inaccessible because twigs had grown over some crucial bridge tiles, blocking passage.