EDIT: First of all, thanks to Meph for putting in time and effort and asking us for suggestions. I have played this game for about 6 months, having discovered masterwork two months ago, I must say warlock and the rest of MW are the most fun I've had with the game yet! Though if I am wrong on something or don't have a grasp on what's possible with the game, please feel free to correct.
suggestions:
on the topic of birds and flyers: perhaps the orrery can be used for an x-soul reaction (unsure about balance) that "call storm" or "create gusty winds" that temporarily knock fliers that are outside out of the air?
on improvements and changes generally, regarding meph's earlier post and reddit post:
1) removing the functionality of the graveyard and hoardmaster might be for the best, currently graveyard is more of a crutch for starting fortresses to create resources out of thin air, and hoardmaster sees almost no use due to that it's only attractive at early start to squeeze out a few more souls out of presumably wood, the easiest trade to fullfill, or only usable in lategame, to get rid of big stacks of unused resources, but by that time you should have other reliable ways to get souls.
Graveyards could be turned into decorational structure for the moment, and hoardmaster sprite could be used for a new building, crucible of power (see next point).
2) military organization can sometimes be a bit of a pain when you are forced into the current squad structure dictated by nobles. I am referring to the horsemen of the apocalypse, as well as the ghoul master and crypt lord. I do like the fluff they bring to the table, though, and their sprites.
Perhaps these titles could be set the same way the overlord is transformed, using a building ("the crucible of power") while regular militia captains are put back in? maybe turning them into these super-beings uses some reagents too, and buffs their skills? They could become part of special castes in some way to make sure their sprites display right. I dont know. Is this how it currently is done? Would like it if any civ member of any race was allowed to become them, I dont know if this is possible already either.
3) Skeletons having innate mining while not learning other skills. This is cool and all, but due to the way DF handles job-related equipment, its always so frustrating when my squad of skeleton archers drop their bow to the ground, turn into miners and go to pick up their pick and vice versa (when they are assigned or relieved from any movement or defend burrow orders).
Instead, why not add extra skeleton castes too? Each gets a different innate skill they specialize in and they still don't learn any extra without inscription. Monotonous tasks would be assigned to them, as well as combat skills that get them out of the direct line of fire, such as mining, gem-cutting, archery, metallurgy/weaponsmithing-stuff.
4) While on skeletons, I feel that warlock gameplay should be more about resource recycling, a sort of "tiered unit approach" where skeleton is the base you can fall back on. What I mean is that currently skeletons can be re-raised, as well as warlocks, but these new units you're envisioning and current ghouls can't. Worse even, they can't be butchered. I don't know if this is hardcoded into butchery or not (that you can't butcher your own civ) but perhaps a custom building can be of service. Something that takes in corpses of all types, even own civ, and produces souls and either limbs for ghoulcraft, or bones + flesh + scalp.
You won't be able to raise your ghouls that died in battle back, but at least you can create a skeleton out of their corpse (either one of a randomly chosen skeleton caste or a final caste that has no skills*). To save yourself the effort of building death trap rooms for your own units, there might even be an option to "vivisect living unit", tasking somebody to enter the machinery and be slowly stripped of skin and flesh, producing a bunch of it to be used, and most importantly preserving the skills that it had in life in the new skeleton (this is the payoff of doing this pre-emptively instead of waiting till they fall in battle, as well as the way to maybe get magic-casting skeletons i.e. liches). All civ members can also just do a reaction at this building to get themselves killed, in case you have some kind of need for that (skeletons included).
This would add a whole new layer of depth to skeleton and soul management. Are your ghouls/warlocks starving? Get one of your ghouls to be skinned alive to feed the rest, before they all starve. Are you one soul away from buying that awesome something you wanted? Get a skeleton or somebody else butchered. Did you diligently slaughter a whole invasion or ambush force? Perhaps you should create skeletons (or the new zombie units) out of them, and after they're done helping out with your build project they get turned into filled phylacteries and ironbone equipment.
(*I dont know if when this system is implemented newly raised skeletons should have innate skills, because "rerolling" your undesired skeletons into new ones might be unbalanced)
5) With all these changes to skeletons, to fiddle with the balance I wouldn't mind if the ironbone/bloodsteel upgrade system was taken away, as well as the pylon control. It's just very tedious, especially when miners dig out rooms in the worst way possible, cutting LOS. Instead, perhaps the control crystals should cost a bit more to make and be able to turn the unfriendly undead raised by the necro circle into undead that are not controllable but at least won't attack you.
6) Under this new system of prisoner taking, perhaps can we take the prisoners and turn them into warlocks too? An interesting angle would be either magical hypnosis/stockholm syndrome, and kidnapping of children (adding it as an extra raid target, as well as "plunder graveyard" for corpses) to turn them evil at a young age and wait till they grow up.
Finally, as a personal request, can regular whips be put back in for production? Metal and leather ones that you can make at the leatherworker. It's mostly a fluff thing for the mistress. A scourge is just not the same. I was also going to ask if levers could be attached to coffins to dismantle them when activated (for purposes of mass reanimation) but it seems that from a previous post, corpses can be reanimated inside their coffins.