Not sure if it's been considered before (or if it's even in the new version or something) but I think it would be great if cave tunnels had a height to them, the same way creatures have height. If the height in a tunnel is lower than the creature's height (ie. human is 7, dwarf is 6), than the creature has to always crawl to move around in it. A miner can mine tunnels up to 3 sizes higher than their own, so dwarves could make size-8 tunnels, which would also hold more water when flooded (I believe in the new version you can fit 7 'layers' of water in a square?). If a creature is more than 5 sizes larger than a tunnel they can't enter it at all.
I think this would add a whole huge new dimension to the game itself, allowing a nest of kobold warrens for example to be completely different from a dwarf cave. It would also give vast possibility for things like base defense (dig a 3-height entrance tunnel and force invaders to crawl through or turn away entirely!), or making crawlspaces. In addition, you could fit more into storage squares if the height is bigger, like bigger stacks of items. Perhaps dwarves would also get happy thoughts if rooms have high ceilings, particularly their bedroom, or you could order your engravers to 'vault' the ceiling so it's much fancier (or even engrave the ceiling itself!)