On the headshot bit, I personally think we should move in the opposite direction, where the tougher zombies can actually survive losing their heads. Or, if not survive it, not have it be a permanent problem.
Remember, these zombies are not really using those heads of theirs for much beyond sensing stuff, the actual motivator is the subprime ichor, and the zombies are taken down by loss of homeostasis rather than any sort of organ damage - to that end, chest shots are actually likely to be more effective against them than headshots.
There’s lots of interesting places we could bring this later, and it makes a lot more sense than the “headshot” mode and is (if I get my way) more the direction we’ll be going in.
For (1), I’ve had the same idea, but the main barriers there are fairly technical. I would like to see something like this, at least, for more “advanced” recipes, and I think the idea of a skill cap is a decent one.
For (3), we’ve got the roaming mob system planned, which should serve to repopulate cleared areas if they aren’t maintained, and the zone system which might repopulate them with things other than zombies, but both of those are a ways down the road if they happen at all (with roaming mobs being far more likely and far more likely to happen soon than the expanding zones)