So, I've got a lot of ideas, but I don't want to flood the board with a bunch of topics, so I'm just going to combine them here. I'll update as I think of more ideas.
...Somehow I get the feeling that these are going to be ignored (if not by the forum, then at least by Toady), but meh, may as well post them anyhow.
Now, now, don't be so negative.
AI: Dwarves knowing where other creatures are when digging
By this, I'm mainly referring to the, um, "quirk" dwarves have, where they're perfectly happy to channel the ground right out from another creature's feet (or another dwarf!), which often leads to injuries (from a single z-level fall 
), and on rare occasions, deaths. This makes flattening a landscape either take forever by having one or at most 2 dwarves channeling, or be incredibly perilous for your dwarves.
Single z-level falls do not noticably harm creatures. Aside from this, yeah, a bit of knowledge about what's going to hurt people (e.g. removing constructions in such a way as to cause a cave-in), but it'll take a while--the game needs to be able to distinguish between "stupid" and "what the player wants."
AI/Combat: Backup weapons for marksdwarves
As the wiki states: "Although it sounds like a cool idea, equipping a marksdwarf with a backup shortsword just in case doesn't often work, as dwarves are just as quick to run up their foes and start bashing them with a crossbow as they are to draw their swords and do it properly." This seems exceptionally silly to me. I propose that the AI be modified so that if the dwarf has another weapon equipped alongside a crossbow, and they run out of ammo, they switch to the other weapon.
Not a bad idea overall, although crossbows are decent weapons in melee against unarmored opponents, especially if metal (their large contact area means they hit vitals more often).
Interface/Combat/AI: Choosing attack strategies for the dwarves
Now, anyone who's played DF for any halfway-substantial amount of time has likely run into incidents where a dwarf has tried to do something silly, such as grapple a hydra's toe. I propose a system where players can command their dwarves to attack enemies in a certain way. ...ugh, I'm so bad at explaining things. Here's some examples of what I mean.
Go for the kill: Dwarves will prioritize attacking the head, throat, and (if they have a stabbing weapon, particularly a spear) stabbing at where the lungs and heart are.
Cripple it: Dwarves will aim for the arms, legs, and wings, to try to render a creature unable to move or attack properly. They would prioritize slashing attacks when available, to outright sever limbs. They might occasionally try to gouge out the enemy's eyes.
Smash it apart: Dwarves would prioritize blunt attacks over edge attacks.
Aim for the weak point: Dwarves will try to aim for the least-armored part of an enemy's body.
You get the idea.
Good idea, complex, eventually planned.
General: Size representation
I personally think that huge creatures, like dragons and bronze colossi, should actually take up more than a single tile, and maybe even more than a single z-level. It just seems silly that a giant dragon can fit down a corridor only wide enough for a single dwarf to fit down. In addition, tall enough creatures, such as- again- the bronze colossus should be immune to drowning from 1 z-layer of water, but be submerged by 2. (I know that bronze colossi don't breathe, but it's the principle of the thing.) On top of that, tall creatures should be able to step up single z-layer cliffs even if they don't have ramps or stairs.
Planned, but it'll be a while. For instance, even ignoring all else, think of interface issues. How do you represent a nine-tile dragon, or a three-z-level, four-tile colossus?
Combat/Interface: Assigning civilians armor
One thing that's always bugged me is that you can't assign dwarves armor unless they're in the military, leaving them almost completely unprotected during something such as an ambush. I suggest that players should be allowed to assign civilians armor, or even better, assign them equipment.
Yeah, it'd be nice. I'm not sure how many forts have armor to spare, though. Maybe the ability to assign equipment dwarf-by-dwarf?
AI: Cleaning up
Dwarves seem to be resistant to the idea of cleaning and putting clothing where it belongs, and so on. When they're told to bury a body or dump a rotting goblin corpse, they should actually do it, not just kinda put it off until there's nothing else to do. I can't count the number of times I've had to unassign every single job except for burial just to get a single dwarf to bury someone, and even then they don't always do it.
For me, dwarves are perfectly willing to dump items and do other hauling, even the non-haulers, whose hauling labors need to be turned off. (The exception, of course, being those dwarves without functioning hands.) It works well for me.
Combat: Throwing
Do I need to explain this one? ...Yes? Fine, fine... Throwing is hilariously overpowered. You can injure enemies by throwing teeth and even WATER at them. Obviously, this needs to be balanced. (As much as it pains me to say it, because throwing in Adventure mode is a godsend.)
At high skill levels, sure. At low ones? Good luck even hitting.
This issue has been WAY toned down since the old days, when a fluffy wambler could decapitate a bronze colossus.
Pathfinding: Jumping up small ledges
If a dwarf has functioning arms/legs/hands/feet and is at least average size, they should be able to jump up and grab the edge of single z-level cliffs, then pull themselves up... or occasionally fail to do so and fall back down, possibly leading to fun if you're really (un)lucky. This goes double for Adventure mode, where short cliffs constantly seem to get in the way, at least for me.
Dwarven parkour? Um, no. I can see elves and goblins climbing up ledges, but dwarves wouldn't unless they had to. I agree with adventure mode, but how many 1-z-level ledges are there? Oh, and BTW: Planned.
General: Grasping categories
Grasping mouths, tails that grab by wrapping around the item/enemy, grasping feet, and so on, all of which would be independent of one another, so that you couldn't, say, dual wield a great axe with your mouth and tail, as well as item restrictions so that you couldn't use a shield with your mouth.
You try holding a knife in your mouth or foot. It's better than nothing (like if your hands have been disabled), but knowing dwarves, they'd stick their axes in their mouths despite the combat penalties. Maybe mouths could be used to sorta-grasp for dwarves that can't hold things in their hands, but that's about it.
Combat: Knockback and throwing/firing across z-levels
Being able to shoot over walls in an arc, or getting knocked skyward by an attack. Fairly self-explanatory.
"Getting knocked skyward by an attack?" Unless you're a cat being attacked by a bronze colossus, an adventurer being thrown from a dragon's maw, or Team Rocket being zapped by Pikachu, there's no way that'd happen. You can get knocked over and back, and sometimes even flung a bit into the air with enough of a size differential. Arrow arcs would be neat, but (seeing as you can't see your target) not much use, so it should wait until projectiles fly in better arcs.
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