I know we already have llamas as a mountable animal, but what about some giant desert spider or like a centipede that could maybe attack on your behalf when not mounted?
Wild animal taming? As it is you can just mount any llama you find in the world, but what if there was some work tied to it?
Possible animal variants? Like a fat llama is slower but could maybe block some damage while riding, a thin llama being faster but could also die easier.
Weather types. Being out in the sun in a heat wave is deadly, so is a sand storm. Maybe a really nasty rare flood that messes everything up.
Group upkeep while traveling. Party members, animals, weapons, most of it is there already, but adding some depth like needing to carry extra rations for party members and animals.
Animal outfits/gear, like a saddle bag for your llama that lets you do... something. As it is you can pick up infinite supplies
while in the field.
I saw someone else mentioned a shovel, but what if it could give a random bit of loot as well when you dig? As if you find something buried in the sand.
Maybe a bit more granularity in the crafting? Especially for top tier stuff. Making parts for other things basically, that you then combine to build the main object.
Environmental hazard areas? Quicksand, radiation, giant mutant (sarlacc from star wars) nest?
Movement speed over different types of terrain, kinda like Rimworld. Maybe have gear you can craft to move faster over the endless sea of sand. Or just mount certain animals...
Maaaybe a combat oriented version of the whip? Chance of bleeding and/or stun damage on hit, faster than a spear with maybe 1 more tile of range, a weak but very fast weapon.
Weapon mods in general. Not Borderlands crazy, but ammo types, shotgun choke, muzzle brakes, maybe different scopes.
A long range rifle, like with a scope, that can give a further look distance maybe? And maybe binoculars or something, also giving bonus vision range on the map while traveling.
Player needing to eat and sleep regularly?
Drugs, maybe some unknown food items you can find in the world, that could lead to some really surreal desert trips. Certain mushrooms or cactus could give you these items? Maybe integrate a hallucinogenic trip into puzzle sections? Rare and expensive.
Unifying all of the build/electric/shop menus. Q and E doing similar things in all situations, like in the shops Q would -1 to inquired items, while E raises the number.
More building materials. Sandstone, clay, mud, maybe animal sourced materials?
I got like a billion more suggestions, but I'll hold off for now.