That's what I also thought, as I decided to go with this approach:
1. The enemies in the location before have "professions" that change their stats slightly, along with making them more immune to a type of damage, e.g. a miner bandit that has a slight physical damage resistance, or an electrician that has a slight electrical damage resistance.
How would the player know these immediately, or remember them? Do you have this for every profession in the game? What about Accountants? Things of that nature? There's a staggering amount of jobs and now I'm worried you're going to be approaching "Guide Dang It!" territory here with how your enemies work.
I assume the Electrician takes less electrical damage from all the insulated gear they wear... but wouldn't that make them slightly resistant to cold as well, since the gear they're wearing is insulated?
Are you going to fight a lot of Electricians in the game?
3. Connecting to pokemon, enemies have "natures", which are like these in base ElementStatusCore, but with an additional effect of lowering/increasing resistance to one type of damage respectively by 5%. Good if you learn it, but if you don't, it won't change too much - bosses are excluded from this mechanic.
If it doesn't matter to the player that much, why is it in the game?
Does the 5% extra damage ever swing combat one way or another? Does it reduce the amount of hits that are required to put the enemy down? I'd wager "no" if you're saying it doesn't matter to the player that much. Which just brings me back to, "then why waste time having the mechanic if it's not important?"
You might want to step away from "rule of cool" and start considering "what do I want my players to do, because this is in the game? Does it make them do that? Is it fun?"
Even in Pokemon, the "Natures" are largely useless to everything except min/max in competitive play. It's not a very good system, even in that game, as it largely contributes less than even IV's and EV's do. Pokemon is a game where the most damage you'll do is based basically on Levels and Type Weaknesses and everything else is "tertiary".
So, I'm not sure what a multiplayer mechanic will do for a singleplayer game.
4. Throwing wrenches into the gears? Like, what about a tanky general that has an army so big, that defeating the troops she summons is meaningless, and the player should resort to things like freezes and stuns on these, and only directly damage the general (while the game tells them that)?
Depends largely how it's framed. If the standard enemies are dangerous enough to need to be stunned and frozen, then it would work. If they're "easily ignored", then most players will focus down the boss anyway. Or, just land AOEs constantly if you have them.
5. I want to signal major elemental resistances to the player - either as a state that the player can peek into, as a visible thing (e.g. a shield with an appropriate colour), or as a natural association (it's a plumber, so probably takes less water damage), or even as the environment (it's a cold region, so people from here are more impervious to cold).
"Natural Associations" are going to be difficult. I'll tell you that up front. "Water puts out Fire". Why doesn't Earth put out fire too? Or wind?
Fish are weak to Electricity. They're not weak to Fire too? Or any weapon damage? If they're only weak to electricity because "they live in water", well, now you have to consider that for every single enemy there is. Every enemy would be weak to Wind because you could "Airbend" the air away from their lungs and suffocate them. The act of suffocation would render them unable to act in combat as well.
"Natural Associations" is something you might want to steer away from if possible. What you want to do is teach the player every weakness and which enemies they should expect that weakness to apply to.
Use Crono Trigger as the example: "Thunder stun all dinosaur, you know?".
Signposting is important. Even I do it quite a lot.
"Wolves are afraid of Fire. If you burn them, they run away!"
Cue Wolves that when you inflict the state of "Burn" on them, they run from combat.
I even advertise my "Revenge" Mechanic that all the bosses in the game have.
"It's dangerous out there. If you run into a very powerful monster, you should beware that they sometimes seek Revenge when you hurt them really bad. If you hit them with a type of damage that they really hate, it hurts them a whole bunch, but then they attack you really hard in return!"
Then, the first boss teaches this mechanic in action. It's a "safe" sort of attack that merely "stalls out" the player, rather than destroys them, so that they can learn.
The mechanic is just "it does 150% more damage if hit with their major weakness" rather than the "100%". It's enough to shave turns off of combat, but it can cost you turns as well if you aren't prepared to deal with it.
6. Also, the final boss of the nation I'm currently working on isn't evil for the team - they just want to test them if they're worthy (and strong) enough to take the later parts.
Are these good ideas or I'm again misguided by myself?
Is the Elemental Weakness thing used throughout the entire game? How so? Will it always be required to win combat? If not, then why? Can the weaknesses be bypassed?
Here's my experience with Final Fantasy 13:
"Hey, here's a Break Gauge. You need to fill this to do any sort of appreciable damage to the enemy and get anywhere. So, you should learn all the weaknesses".
Me: "Or, just get massively overpowered for this stage of the game, avoiding all unnecessary combat since I can't make my Crystarium any more powerful right now, and use Summons frequently to avoid having to engage in the Break Gauge mechanic which makes combat take forever".
You need to be very careful when you implement systems like that. Systems that are very "all or nothing".
If I must engage
in the mechanic throughout the entire game, then you need to make sure that the mechanic is fun for the entire game. If it grows stale, or boring, or gets time consuming... Then the mechanic actively hurts your game.
If the mechanic is optional, then you need to decide if that's a good thing to be optional, and whether or not the mechanic should exist at all, if the players never need touch it.
You'll want to Test Play your game and look for, "Can combat be won by just mashing attack or using the most powerful skill available?". If yes, then you might want to consider doing more with the combat system in order for players to "engage" with the parts you want them to engage with.
As a player, if I have to expend MP every single round of combat to win, then there are going to be points where I run out of MP. Or, need to carry a ton of Consumables to restore that MP. There are "knock on" effects to everything you do as a dev.
For anything you implement, you need to answer some basic questions every single time.
What behavior does this mechanic make the player engage in?
Is that desirable or the projected behavior?
Is that behavior "fun"?
You will want to run Test Plays of your game frequently. With strangers if possible (friends and family will tell you things are good, even if they aren't). You will want to watch them play and note their behaviors. Add nothing as you watch. If possible, just record their gameplay and not be in the room with them, saying anything about the game. You want to see what they do, and figure out why they're doing it. You don't want to "taint" the tests by offering your input or yourself as a distraction.
Does that make sense?