Down the lines I really want to look at how populations will shift. Soon you'll be able to clear out packs of beast, say all the wolves. And for a couple days youll have free range to do what ever you want as it repopulates.
Something with that system though I think would be neat, would be migration. Like a single rogue the splitjaw comes up because it turns out theres no more predators up there. This could like you said considered a boss, have its own quests tied to it, etc.
Would certainly add a more dynamic flair to exploration in general. Do you deal with more frequent but less deadly annoyances like the wolf packs, or do you eliminate them and then have to deal with whatever scavengers come to pick them clean, or any opportunistic migratory beasties from lower levels like you said. As far as tying quests to them, I think that'd work pretty well for unique encounters, a particularly intelligent or belligerent example of whatever critter's species wants to snack on your entrails, with weaker versions as radiant quest enemies or minibosses after the first big hunt. That or maybe it could be the opportunity for a Moby Dick styled encounter, where said critter permanently injures you or causes some sort of catastrophe that has you or the Association swear vengeance against it.
That is the main reason I wanted to move away from randomly generated characters. Their will to some point as you kill them off, and I need to boost up the population, Human as well. But any you encounter you could meet again, meet again. The one which takes your virginity, or like you said, you lose a limb or eye to them. For that one day where you meet them again, this time much stronger... Or at lease you hope so, they take the other arm and its time to throw in the towel. Well kick it in.