* Learn-by-doing: so much more immersive. Skill books could be rather rare and used to unlock the next tier of skill. Magazines and crafting notes would be more common and could be used to make a book - perhaps 4 notes/mags of the same skill could be use to make a skill book. Tier one could be level 1-19, T2 is 20-40, T3 is 50-70, T4 is 80-100. Exploits are easily overcome by limiting each crafted good to a certain tier. Your stone axes would give less and less skill the closer you got to T2 and none once you unlocked it, although their quality would increase with tier mastery. Many games use similar mechanics.
* Weapon parts. Would like to see this come back and be expanded. Many mods could be re-imagined as different types of parts, or still be mods built FROM manufactured parts. Some mods simply shouldn't be craftable otherwise (laser sites, scopes above 2x power - basically stuff that relies on electrical components you can't field-produce, titanium steel, etc). However, if we also brought back advanced tools, perhaps one for each type of crafting, then I could see people with nearly max skill building pre-apocalypse components on a limited basis. Might need advanced workstations for this.
* Believable building material progression: cobblestone bars? Really? For mostly-solid, mostly-square blocks the progression could be wood frame > solid wood > cobblestone > iron plated wood > iron frame > concrete > steel-reinforced concrete > steel frame. Blocks with really odd shapes or a lot of airspace in them would go wood > solid wood > iron frame > steel frame. Most solid steel blocks really never made sense if you think about it but steel cladding would still be cool. I could also see plastic being used this way: melt it down into thick plates and you've got something that's quire resistant to getting beat on (though not much use against bullets or bombs).
* This may have been a mod, I'm not positive..but I remember eons ago repairing individual components of vehicles. It would be cool if tires, engine and other parts had separate durability. Bonking into things would harm the frame, driving with turbo on would slowly wear on the engine, suspension (if it were added) would take damage from playing Dukes of Hazzard, etc.
* More challenge in finding ore: frankly, you'd be hard-pressed to find an iota of surface ore, other than the odd coal seam, anywhere near civilization. I wish there was a prospecting skill or something that worked sort of like treasure finder (or whatever that perk is called). You could have one for metals and another for minerals. For multiplayer this makes your miners even more useful, although with solo play it might turn into a required skill. I wish I could think of a happy medium. At the very least I'd make those "ore boulders" extremely rare so you'd have to go looking for the actual ground patches. If they could be hidden by grass, all the better.
* Aimable spotlights. Again, this might have enabled by a mod. or its lack might even be a new bug, but I can't aim spotlights any more in camera mode. I kind of wish we had auto-aiming robotic lights, too. They could lock onto the first thing that enters their field of view.
* Caves. I know there are some BIG underground POIs now (one I found was really tough to navigate). But if the odd random cave could be made to appear that would be really cool. The most logical spots for them would probably be cliffs.
* Glass Jars: I'm sorry, but they just make too much sense. Logically the stacks should be small because their kinda bulky (I'm thinking 5), but not being able to collect or boil water is an immersion-killer. In a true survival situation, if you have containers, a nearby water supply and half a brain, water is not an issue. Melting them down for glass was also one of the more believable crafting recipes.