Such as my bullet example up in my original post. Different ammo "conditions" that can be broken down and then put back together to get to the higher quality ranks, kinda like NV.
Lots of drained microfusion cells in the world - chance to cause laser rifle to overheat and need a combat reload.
A harder to find "normal rank" microfusion cell that works as intended.
A very hard to find overclocked microfusion cell that can hit harder or has higher armor pen.
You still have to scav out in the world to get the ammo, or the materials to craft them yourself, and before you go out into the world it'd always be a good idea to break down the junk stuff to craft something that would be more functional. It'd have an effect on combat that could be worked through or around depending on your character, and if it makes sense for that character you could get into some of the more exotic stuff like what NV had. Something along those lines is what I'd like to see.
At any rate, I think weapon degradation is too central a mechanic to the game to just give it negatives/menu-management pluses. I absolutely agree with you that not caring for your gear should have a negative effect on the player, and I don't think things like weapons/armor should be a "forge and forget" system where you make it, equip it, and just forget about it. But this ties into why I'm not a fan of the hardcoe mode in NV as well. It's just fighting a bar graph in a menu.
Things like eating and sleeping should be important and adding them should help immerse yourself in the setting, but in my experience it was just another bar to fight. It wasn't fun for me, just another thing to make sure I'm stocked up on, which I always easily seemed to be. Do I think the idea should be abandoned? Not exactly. Every few characters or so I'll kick on hardcoe mode again, cause when all those systems are tied together like that they kind of give a survivor-esc feeling that I might pass as a pro, just barely. Yet at the end of those playthoughs, I never liked how it felt to have those bars looming overhead. The timescale never made sense and felt gamey. You could pound 24 packs of nuka-cola in seconds and all of a sudden go from drowsy to perfectly awake.
If FO4 gets a hardcoe mode as well, I'd prefer to see weapon degradation there if it is included. Again, I'm not against what it's trying to do, but if it's just an endless fight with a bar graph I'd like a way to not have it in my game.