I have something over 500 hours so let me break it down:
1. "How come Throwing is the de facto best off-spec as it offers grenades for every single enemy type + group size? -> effectively just completely breaks rules 1 and 2 as a single off-spec skill just counters everything."
Grenades are a crutch for whenever your build cant handle groups, specific enemies or stealth enemies, if your build handles those parametres or you just go PSI you dont need throwing.
2. "How come Stealth is the other de facto best off-specc as you can completely avoid enemy types or groups you can't/don't want to fight, or get the drop on enemies? -> completely mitigates 1, 2 and 3 to some degree"
There is only a few characters i used stealth on, if you have high enough movement points/initiative you can get a drop on the enemy by going first, plus more often then not you want to take any fight you see for more EXP, otherwise stealth is only really good in the final boss fight and for specific parts of the game that can be tackles in a stealthy maner.
3. "How come any ranged build inherently gets the PER benefits, something every other build has to fight for with items and buffs to counter invisible enemies/traps?"
As far as i remember there is only one unavoidable trap in the entrie game and that is in core city sewers. If you want to fight off invisible enemies literally just walk in to them or use yell. You dont need much past that to kick them out of stealth. Also Escape master is great at getting out of bear traps if you do get caught.
4. "Crafting obviously is a hard requirement as you can craft the best items, including ammo, grenades, traps, consumables + you can craft important items like e.g. a tactical vest/with psi beetle very early and thus have a far better/easier early game"
Crafting is completely optional and i have beaten the game multiple times on characters that did not have a single point in crafting because they didn't need any, playing with specific weapons in mind especially. In addition you can get high quality "essential" gear for some play styles from certain enemies in the game. Just recently i started a sword character, zero crafting, went through depot A like hot knife through butter because very often speed compensates for lack of defence, also evasion and dodge can save your ass as good as any piece of armor can.
5. "Who the hell thought a random vendor inventory is fun in a game that pushes crafting to such a degree, and then not even offering a means to manually reset the inventory outside of using Cheat Engine?"
Random vendor inventory is requiered because parts have quality assigned to them, the game would be boring as hell if you could just go up to a random vendor, buy the highest quality part that he has every single time in stock and then never visit him again, and do so every time you play the game. If you want THE BEST gear then merchants are note even the best place to look for the highest quality parts.
6. "Why the hell does Bear Trap have no skill requirements while offering big damage, instant and DoT, and a 3 turn root to carpet-trap whole areas before engaging combat? -> just breaks 1-3"
Bear traps are a crutch for builds the same way that grenades are, they require setup out of combat and you can cheese the game with them if your build is too bad at handling a certain kind of fight, if you want to carpet trap the entire place in bear traps then by all means, if you have a good build then you wont need to place a single bear trap in your entire playthrough. Also my energy pistol character that crits for 5000+ damage would like to have a word with you on what you consider big damage.
7. "Why the hell do AoE PSI abilities have a hit chance? PSI inherently has to invest a lot of points into INT and WILL, low CON, low-ish PER, and has to juggle PSI points during combat, and then you're "rewarded" with missing your AoE spells?"
Single target abilities for PSI are already a guaranteed hit with no miss chance and on top of that PSI builds were broken beyond any doubt. Everything needs to be on about the same power level, even grenades with absurdly high throwing stat can "miss" by a few tiles, a guaranteed 95% shot can miss, you can miss on your third unarmed hit and miss your combo. Same can be said about making a sniper build and some times missing those big shots, yes it can happen no matter what build you go for.
8 "Depot A: after being forced to redo it a few times I understood that it's not that difficult, it's just that the level design completely breaks with the previous one up to that point of large areas with plenty of space to move around. Now you have to fight in small spaces and corridors with little room to retreat, where opening doors will immediately put you into combat with 4-5 enemies"
You have to addapt as a player to different situations and depot A is a teaching tool for that, its the first speed bump in the game that basically tests you to be able to handle situations presented here, either you are good enough at dealing with them as a player, your build can handle them with ease OR you brute force your way through.
This is your first playthrough and you are only level 16, its way to early to claim that something is OP just because you feel like it.
"You have to be able to handle organic and non-organic enemies"
Builds can use different weapons for different needs and can simply swap to a weapon that can deal with a "non-organic enemy", even throwing can do that now with shock shuricens. The only build that cant handle robot enemies is a build that exclusivly uses mind controll PSI.
"You have to be able to handle single targets and large groups of enemies"
If you can kill enemies fast enough then you can handle groups without much issues, otherwise in the words of a wise FPS boomer: "We do the wolfenstien 3D strat, bottleneck and blitzkrieg" aka find a single tile passage, run in and behind a corner, watch as they line up and block each other from entering.
"You have to be able to deal with invisible enemies and traps"
You can avoid every single trap in the game by walking around it, invisible enemies can be dealth with by simply predicting where the enemy is and then walking in to them if you dont have perception.
"Crafting for the best items"
Best items that have quality variation, yes. And you can get exactly what you want out of the gun or armor you are making, or you can just use unique items that are already available in the game as a supliment, plus they give unique stats and bonuses, just boils down to what you need to get out of your guns and armor.
Skill-based system which affects hit-chance, damage and requirements to even be able to use an item/weapon
You get enough points with 30 levels to invest in to everything you want and still have leftover points, the only limitations you really have is stat points, and at that point it comes down to build planning. By the time i start the DLC im already level 26+ also you can go for versatility if you want to test stuff and be able to use every weapon in the game without the need invest in to separate skills.
Also let me humor you: "why, even for non-dominating builds posted in this forum or Steam, is there almost always throwing selected, even when the build itself isn't using throwing as the main damage source? It's almost as if the skill does counter every enemy type + group size while only having to adhere to the same design principles as all the other skills, right?"
Or because people need a place to toss leftover points and other skills are usless to them on the build/they need a ranged option that is not a gun for dealing with enemies they cant reach because they are doing a melee build/having constant scatter on grenades you throw from time to time is infuriating. If grenade miss chance lowest value was capped at 50% most people would never invest in to throwing as about the only 2 things that require throwing to be usable are nets and throwing daggers. Its not like you need throwing skills to use grenades of different types. And at this point it boils down to -> "Grenades counter every enemy type + group size" Not "Throwing counters every enemy type + group size" as i can still use grenades without investing in to throwing but you cant use throwing daggers and nets without throwing skills.
