If When you add omega station to the game, I think it would be neat if the entire station was pitch dark with no power, so you have to bring light sources/NV in order to explore. If not omega, then a multi-level dungeon or series of maps somewhere, maybe in infusion. If omega, have a str 20 check to open one of the unpowered gates (maybe have it be slightly cracked open now; could be str 16-20, but there's tons of str buffs now), maybe in addition to that beetle map east of the rig with a mysterious wall that totally isn't a secret back entrance.
In DC right before the labrynth there is a cave full of rathounds. Near the labrynth entrance there is a small crevice that you have to go around; why not make that an agility check to jump over?
In the river map right outside Oculus, an agility check to jump the river at the south end near the rail crossing train map exit. Make it a higher one, like 10, and maybe keep that siphoner on the other side from jumping out until you get across.
There are a handful of areas in the game that repeat players pretty much always avoid unless they are playing on classic or are hunting down specific enemy drops. Assuming you haven't done so already, I suggest making these locations for random encounter containers (like the mushroom brew bag or one of those hacking boxes, or a dead body). The early-game upper caves burrower map is the first one that comes to mind. The lower passages death-stalker map, the black crawler lair, hopper island, etc, would all be decent ones.
In the early game, especially in the areas closer to SGS, maybe add random encounters of rathounds, psi beetles, mole crickets, stalkers (not death-stalkers), etc, maybe only on hard and/or dom. That crossroads map outside omega's main entrance (from GMS, one map east then north) seems like a good spot for random encounters (of any kind, not just fights) but I've never seen any there.
In lower underrail maps with roads, there are sewer grates along the sides of the roads. If you think it's worth your time, maybe make one of those a perception or strength check to enter, with a tunnel down there. Maybe a short vents-style area with some random loot/enemies/traps. Or maybe make it connect to the under-passages?
A random fragment with a mole-cricket horde/hive and a queen boss who drops a 1 point oddity? I know mole crickets are meant to be the merest of early-game obstacles, but a surprise map that makes them kinda challenging would be neat, I think.
Adding a guaranteed, but randomized-location item/container in the early game in places repeat players usually never go to.
Like: on the old jonas map in those little dead-ends, in the outposts behind the buildings, sgs in unmarked container in unused area, under/across from the sgs train station, etc
Tying in to that:
Have you considered unique footwear? For instance a pair of old-world sneakers?
Unique helmets? Like a dirt-bike or motorcycle helmet?
Either could make good early game loot; I could see sneakers giving +2-5 to persuasion for a nice almost unique bonus.
Speaking of unmarked containers in sgs, you could add something helpful to 1st level characters for the outposts quest, like a small amount of 5mm jhp, or a mining helmet.
