Likewise, if we're talking about noxious gasses, then there are topics of air quality I remember on topics like phlogiston, or "depleted air" which this seems to play into well. (I.E. dwarves hit trapped pockets of toxic gases, and/or we get closer to concepts like the need for ventilation shafts and re-oxidizing subterranean "plant"life.)
I'm not sure too much realism with regards to ventilation is a good idea. The problem is that ultimately, traditional fantasy Dwarf Fortresses are not plausible; there are a few changes (requiring that people move all that dug-out dirt somewhere, realistically modeling underground ventilation, etc) that would functionally make Moria impossible.
I don't think that's a good idea. The game is meant to be realistic, but I think it's meant to be realistic to the fantasy universe it's intended to generate, which includes subtle changes from our own to make fantasy stuff plausible.
Actually, I'd quite like both of those to be in the game.
All that mullock having to be moved would prevent people from just digging straight to the magma sea, and would make minecarts actually useful for their intended purpose. All we need is code to let the moved mullock consolidate into a waste gravel wall again to make it not kill FPS. Starting fortresses can find ways to just shove it off-site (hey look, catapults are useful again!) and at the same time, fully mature fortresses can probably find ways to dump mullock to the magma sea, which would avoid the problem of an "anthill" fortress.
As for ventilation, it can help recreate an actual reason for different stages of excavation. The 2d game had three obstacles in the path of the fort, with different threats emerging from each that couldn't be easily sealed off. Each threat had to be dealt with in succession. Now, you can just dig around the caverns and not worry. If you make it so that the caverns are pockets of oxygen-producing subterranean plants, there's reason not to just turtle up and cut it off entirely. In the long term, you can set up oxygen-refreshing plants in safe locations, but since that takes time, it can be a risk/reward trade-off that challenges players with more threats if they want to dig deeper faster.