As for mobs and mob spawining, maybe have some sort of ranking system for "spawners"? Invisible or indestructable, and each one spawns randomly a single type or from a "tier" of monsters. Research can use dead animals to build stuff such as sensors or trackers to find that specific animal and it's spawner (or those of a certain tier, the deadliest requiring much death, wow)
If possible, restrict the number of spawners to create something actually akin to an ecosystem, as well as harvestable plants that can't be grown from Botany (because they're rare, or exotic, or what-have-you. Bonus points if you can make them unidentifiable by anyone but a Botanist or someone with Botany access.) For instance, you could have 3-5 Plant Spawners, 2-4 Blue-Level Spawners (can hurt, but either nonagressive or nonthreatening unless in a swarm), 1-3 Yellow-Level Spawners (monsters that could kill an unprepared or inexperienced single hunter) and 0-2 Red-Level Spawners (monsters that are plain impractical to take on single-handedly, even when armed.)
A secondary way of randomizing plants is to create an event that gives an "unmarked" seed packet that only explains the genus of the plant (algae, fruit, etc), and in growing said plant and getting a seed packet from it, you can get the actual seed packet (Red Algae, Dragonfruit, etc)
Tackling the Botanists-Have-Wood issue is fairly simple- remove the ability to get tower-cap mycelium easily. Removing it's random spawning would go a long way to this, unless it's made very rare, which could also work.
Scientists can gain things from certain mobs but this is mostly held to the whimsy of the RNG, though if this is handled through each mob dropping certain values of all-new tech trees, it can be reasonably standardized. Certain drops could immediately warrant certain items- if you kill a toxic porcupine, this could translate into a quill-gun that works like a rapid-syringe gun but with more shots, loaded with a beaker instead of individually (fill it up to, say, 90u, and it fires 6 quills before empty, etc.)
Stuff like Pheromone Grenades that could attract mobs or cause fever and confusion, free Tricord or "natural remedy" items, etc...
Upgrading the Hunter's Rifles should be possible but done through Security or Research, unless it's something like sharpening a stick and taping it to the barrel (as it's assumed these Hunters are rather self-sustaining, and should have such options. I also suggest a one-barreled shotgun and new slug types.) You could increase melee damage with the weapon much higher with, say, a Kitchen knife, or a Stunbaton, but a Hunter could just as easily create spears to throw or use in combat (that probably break fairly quickly.)
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Reloading a spent slug is something a Hunter should definitely be able to do as well, though actually making buckshot may be impossible. Possibly a machine of some sort that takes items and empty slugs, and refills them? Unorthodox slugs should totally be possible, but likely not great at damage (Shards of glass, for instance.)
Also, it wouldn't be SS13 without a few potential secrets. Stuff like a Russian Locker, cultist cave paintings, etc...