ZONK!
Appearance modifiers: I was planning to have a lot of these. Each entity keeps track of the general appearance of its members, and further and further deviations can lead to more extreme results. Nakedness is a definite candidate, as are drawn weapons and missing/extra body parts.
Real-Time: I'm pretty sure that there will be both turn-based and real-time options. The code from the beginning has had the structure for it, although I hadn't foreseen it 
Every step between squares takes your player roughly 100 "clicks", and attacks take fewer clicks and so on. It turns out that these clicks are almost perfect as real-time frame refreshes. Basically, in the turn-based mode, when your character is not doing something, the game will freeze and you can select an action, just exactly as it has always been. In the real-time version, the game won't freeze, and your actions will occur on key presses/mouse clicks. It's really a trivial modification. In the end, everyone should be happy with it. I'm more of a turn-based top-down guy myself, but if it's easy to do and strictly optional, I'm all for the adrenalin rush of no hitpoints/permanent death/nasty injuries/quick thinking in real-time. Just don't expect to make it very far!
Dirty Fighting: Well, you can fight how you want in this game (specifying hit locations by aiming, etc.). The notion of dirty fighting would presuppose an entity having some kind of honorable fighting system. I haven't thought about that much. Entities will have rules set up to curtail certain behaviors, and this could include certain attack types/locations, and things like ambushes and backstabbing. What constitutes an ambush is difficult to say in game terms. Being a dirty fighter would then mean that you have and use knowledge of weak points and ways to attack them that would be frowned upon under the rule structure.
Industrial Global Warming: I'm not sure that the technology/population density would get this serious, but magic messes all of that up, so such a situation is certainly possible. Keeping track of temperature/rainfall/biomes etc. isn't all that difficult (generating them realistic would be nasty, but I'm not too preoccupied with that). In terms of the game, many small sources of heat would be harder to add up into global effects than a few large sources. If I add global warming there would be a noticeable bias in that direction.
Holding breath: We definitely need this. Although it would be annoying to force the player to hold his or her breath every time he or she dives under water (the program will probably hand this automatically -- perhaps through an optional flag), there are other occasions where the player would want to do some breath-holding where the game is in no position to do it for them. Say the player walks into a room filled with invisible poisonous gas. If the player knows about it, some breath-holding might be in order. If they don't specify it, they get nailed.
Casting spells with the... night soil: Yeah, if we go ahead and add those substances, they will be fair game for spells, eating, etc. Every material the program has access to in the beginning of the game during universe creation will be used to make the magical art mechanisms. These kinds of materials will be stored in the species definitions (in the mammal motif, blood is there now, along with skin/enamel-dentine/bone/muscle/various organ tissues).
Game taking over your character: Hey Demon! If the character is drunk (really really drunk) or charmed, I don't have much of a problem with this -- especially if as you say, their willpower attribute is low. I've toyed around a little with the idea of a lack of patience penalty, which would be like the laziness penalty (but instead of forcing inaction, it would force action). In the end, I'm not sure how these personality quirks should effect gameplay. Altering commands is pretty drastic/frustrating, but hey, so is getting your arm chopped off, and we do that all the time. We'll have to see when we get closer if such a thing would add or take away from the overall experience.
UPDATE:
I just changed the type of dynamic arrays I'm using (these should be a lot faster), but the conversion generated exactly 1519 compiler errors (and 1 warning). Uck. It'll probably take 1 1/2 hours of megadull labor to sort that out. On the upside, I have the beginnings of a 3D view in Armok now, with simple rotation and so on. I just need to add the slopes.
How boring.