Have had no issues with caravans. It takes a while for them to arrive. But thats because they wind through to trees on their way in. I havent cleared straight paths for them yet. If youbhad them wind around a lot through some trapped gate systems they might run out of time.
I typically build 5xmax roads out to the edges for the caravans. I rim those with staggered cage traps and dig 2x2 holes right by the edge. Not only does it mean a predictable spawn but I get bonus wild life captures to train up. When I had DFHack working with older large areas teledwarfing and instant jobs let me build covered roads through a huge area with lung-eating mud rain. That was the only spawn I've gotten so far with giant sponges.
For FPS problems with wildlife I put them in an encolsed clay, silt or sand area once caverns are opened up. The only access is through either a ramp or stairs. For some reason the FPS drop never kills me with peacock or duck-splosions using the z-level change like with a regular flat layout.
Having lots of mini-forts sounds pretty interesting I usually made one big fort and another very far down near the magma sea. Get a lot of puke lined hallways from cave adaptation that way, though. At one site I even tried to fight cave adaptation by replacing the entire rock roof of the taverns with green glass. That can be a lot of overburden to remove if your taverns are in the middle of a mountain.
As a benefit of 16x16 you can get multiple visitors in the cave system and not have to worry too much about dwarves hunting spider silk. There's so much stuff for the beats to go kill that you can draft, train and send an axe dwarf team before losing too many people. I keep hope someday to run into a big ant man colony or something similar.
Another map I ran had 6 magma chambers in the first layer alone. That's just begging for magma topped towers. Great towers of flaming liquid death dotting the skyline. Or even whole mini-forts dangling over the magma pool. Although I could do another auto-mincart filed giant lake of fire. Just don't let dwarves train near magma. They can still doge through walls and into pools or dwarf evaporating liquid !!!FUN!!!. (The last time I ever make a magma moat that close to my walls.)
As far as that buggy 16x16 with the Roc, those kinds of megabeasts work like reclaimed forts. They are listed as current resident and will only agro dwarves when in range. The Roc stayed near it's spoils and killed a lot of Giant Eagle Men. As soon as I killed of the Roc the game spawns an instant army for some reason. Save scumming confirmed that this was consistent. As soon as the current resident fell a random army would seige the map.
That's a valid plan once you have the people to spare.
Personally I won't worry about such a large site until I get embark scenarios that give me extra dwarves to start. No reason to be slow when you have so much land.
I got 150 citizens in two years in one fort from waves of large dance troupes. Sadly, you cannot do anything with the performers as they are all nobles. They still seem to pickup random jobs. Performers with skills will get moods. But a two or three wave fort with 30-ish dwarves is already big enough to mine out a full organics processing array and setup fishing, mining and other industries. I figure about 50 dwarves for a large isolated sub-fort would work well. But as little as 4 or 5 dwarves could run a fishing village as long as you have a source for clothing, booze, military and hospitals.