I think a fun idea is the ability to improve the player character with cyborg additions or some zombie/mutant gene mods. Right now you can upgrade your character by adding powerlegs and armor, you make the electrified knife to upgrade your basic knife attack, and you boost your health by eating canned meat. However, I think it'd be way cooler and thematically appropriate to do things like necrotizing your flesh to gain increased maximum hp and bonus health from canned meat, weld those empty cans directly on your dermal armor to patch up the holes, and grow some extra giant spider limbs to increase movment speed and melee damage. It'd be great to progress your character in more ways than simply having the most guns, and if the self-modifications were exclusionary or hard to get more than one of then they could have reasonably large bonuses to create alternate playstyles.
In Teleglitch, you fight against monsters. Why not become one? /overdrama What do you think would be some fun modifications that would fit with Teleglitch lore?