i know some of those things had been said but i wrote this as i play and then read whole topic.
also, Devs, great work so far. keep it up 
so what i would like to see in game? 
bigger focus on survival: ie less edible wild animals, most of them tainted, or less spawning in general. this is especially true to wolves as with their low combat strength they are essentially home delivered snacks with fur. non-combat ways to get food (except for scavenging)
higher melee combat difficulty for certain mobs: slicing down bear with just combat knife is of course possible but…
some more skills that would govern certain aspects of game:
ie. chemistry for making things like drugs, mutagens, explosives and gunpowder,
leadership/charisma for allowing NPCs to follow player orders/faction,
smithing for making tools and building components etc
bioengineering/genetics for help with SCIENCE!, i mean to manage artificial mutation process (on followers or yourself)
security for bypassing those nasty card readers and breaking locks.
creating and managing your army of survivors:
get NPCs followers to act as workers, guards, scouts, scavengers, warriors, engineers, medics, etc, to offset shortcomings of player, combat/defend against enemy factions or just zombie horde, etc. Being on your own is fun of course but shouldnt be as easy.
also, area threat rating: the longer you stay in one place, the bigger chance for horde or attack to happen. so either be on the move constantly, or get good defenses.
making vehicle slide (L…O…R) display work for regular turns as well, and maybe some kind of pointer how much distance will your vehicle cover in next turn based on current speed (accurate based on driving skill)
construction/furniture special options: as making stone/concrete walls, building up special furniture (chemistry workstation for making chems, fridge/cold basement to keep food edible, fireplaces, kitchen, various generators to power up compound, indoors lighting and heating, rain catchers, medstations, distilleries, and probably a lot more.)
crafting in a batch, and repeat last action command.
vehicles! well, yea. helicopters, boats, hovers. this is teh future after all.
option NOT to use integrated tool set heating abilities when other source of heat (fire, hotplate) is available.
bionics that enhances stats.
bionics would require maintenance.
also, mental instability linked to “too many” bionics installed, and/or too many mutations gained. very nasty one given enough time and little treatment.
expanded crafting, with ability to make most of the items out there (with of course need of advanced crafting furniture for many more advanced items)
dungeon mini-maps : paper+pencil, or some kind of computer mapper, 'a’pply to see map of explored dungeon, or just current areamap without LOS restrictions.
EDIT: oh i remembered:
separation of inventory and equipment pages, making both clearer, showing what is worn where, and what is carried in what. storage items working as containers so dropping backpack before combat would remove all items in it from inventory as well.
stacking of items on ground maybe and/or “pick all” command as well.
/EDIT
cheers
