So we're still playing around with this concept so would love to hear thoughts on it.
I've been playing with these ideas for a while. I've considered making a post on it, but I'll post what I currently got here.
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For designing units, each designed unit would have a certain kind of build that it would consider default, but it could equip weapons and other items different than what it was designed to use. For instance, a common knight might prefer an "iron longsword" as its weapon of choice, but nothing would prevent it from equiping a "moon silver katana" instead. Likewise, it could equip something very different such as "bows & arrows" or a "musket".
The advantage of this system is, you could produce and reequip units using different equipment, superior equipment, inferior equipment, or even make them completely bare. For instance, if you manage to invade and capture a town using common knights, and you manage to loot moon silver katanas, you could refit a number of your knights with better weapons in preperation to fend off your opponents from trying to take back their town.
Such a system would make the only real difference between units (of the same species) would be their training, and possibly their magical augmentations.
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The second idea I have is, I want to be able create very powerful units, with or without magic. I want a to make "Soul Knights" (units who have ghostly limbs from dead comrades), "Necromancer, multi-limbed abominations" (necromancers who added undead limbs to their bodies), and Fire-blitz golems (golems who can shoot jets of fire that makes flame-throwers look like matches). I want to be able to make units powerful enough to be a threat to a channeler if they are not careful.
To that end, I would not only need magic spells that I can cast on per need baisis, but I would need persistant magical effects. Lets call these persistant magics rituals. These rituals could animate undead, animate golems, provide ghosts with ectoplasm bodies, and so forth.