Some comments, largely about potential interplay of game mechanics and realism, more than questions...
It would be interesting to see if, when army attacks require the army to be able to get to the map location, deep sites are vulnerable to attack via the underground roads once armies have taken their fortresses. It would also be interesting to see if they have builtin defenses such as shutting gates to those roads or intentionally causing caveins. (Such defenses could be used as a cop-out if there are technical difficulties getting such attacks to work; instead, when a fortress is taken the deep site road to it could be blocked off to explain to the player why no attacks can occur there. Just bouncing possibilities around in my head here.)
It would be interesting if, once you can change the savagery of a tile by wiping out enough of the animal population, killing enough non-savage creatures would change the savagery and cause savage creatures no longer to appear either. You could hand-wave that as a sort of food chain thing -- the savage predators don't have enough prey -- without ever actually adding a food-chain ecosystem mechanic.
If climbing speed and walking speed are set independently, the flip side is that we could have creatures like spiders that climb at least as fast they walk, while normal creatures climb slower than walking. Or, let's say monkeys in trees...
If I recall correct that I heard a while back that enemies can jump if they happen to see that the far ledge is within range, and can climb under similarly limited conditions, but cannot jump to a landing in a climbing position -- i.e. will not jump over a gap if the far ledge they'd have to land on is the side of a wall... then putting a moat full of water (which would have to be passed by jumping, for non-swimming creatures; use magma instead to block all but the fire creatures from the depths) around a standard one z high wall (which cannot be jumped onto the side of) might be a simpler alternative to attempting to set up walls too high to climb over or with an impassable overhang. And then we're back to the so-traditional-it's-stereotyped image of castles with moats around their walls. 8^) (Which, let's face it, worked in real life for a reason. It keeps ladders and seige engines at a greater distance from the walls, thereby boosting the walls' effectiveness.) It might be interesting to make jumping-onto-a-wall a special skill granted only by a raw tag, down the road, so that if such a mechanic is added it doesn't make all creatures into clones of Peter Parker by default, but rather respects the realism of moat-surrounded walls being virtually unclimbable.
I wonder if pathing additions/improvements, especially the whole accessible components thing, will ever fix the processing waste that occurs when animals keep trying to figure out if they can path through closed doors. (Ok, that's almost a question, and isn't about gameplay mechanics vs. realism... eh, whatever.)