SO! In my future campaign in order to justify why PC's feel so much more powerful than a commoner (even at level 1) I have a bit of lore that looooong ago there were a "race/category" of people called "heroes" that were touched by the gods. mechanically, "Heroes" are those with PC class levels. 

The main BBEG is going to be this huge evil God-Emperor who centuries ago exterminated ALL of those born "Heroes" several centuries ago.
Heroes are still born now, but due to the Emperors laws, if a person is recognized as a "Hero" they are killed immediately. Usually this happens when they're young and demonstrate themselves as exceptional, but the occasional Hero slips through the system (the players at the start of this campaign)

I kinda want the emperor to have a form of "Inquisition". like a detachment of knights trained specifically to take down Heroes (Player classes)

So this is gonna get kinda metagamey here, but, if you were to design a monster SPECIFICALLY designed to be able to take down Player Characters (generally) how would you build them? what feats/abilities would you give them?

Ooh, cool idea!

I don’t know about anybody else, but an Antimagic Field and a few Legendary Resistances would completely shut down the characters I play.  Crowd control effects and legendary/lair actions are pretty effective against my players.

I mean... all monsters in the game are designed to challenge and potentially kill PCs. That's what combat is for in D&D. All it takes to kill a PC is to reduce their hp to 0, which even the lowliest goblin can achieve under the right circumstances.

If you want some kind of special mechanic to nullify PC features and abilities, I'd think long and hard on how to make that fun for the players. I'm not sure that's possible.

What I could see is enemies designed to track down heroes. A campaign where the party is ruthlessly hunted could be really interesting. These enemies would have divination spells/abilities like hunter's mark or scrying.

The narrative hurdle would be to have a good reason why the super-high-level god emperor doesn't just teleport to the party when they are level 2 and one-shot them with a fireball or something. Your job will be to make it believable that a low-level party could survive at all with so many high-level enemies gunning for them. Maybe there could be some dissension/corruption within the ranks of the hero-hunters that could be exploitable. 

You'd also want some kind of underground resistance network because who else in their right minds would ever help the party (give them lodging, advice, buy/sell gear, etc), knowing what they are? An allied faction that helped hide/transport them would be very useful.

I think an antimagic field is a definite! Magic in my world is something that WAS big back when Heroes were everywhere. So it would make sense that if a person capable of magic was born, the emperor would have some counter to it in his inquisition.

I think i need to start thinking more meta... like "what makes PC's overpowered" and then "how do I counter that"?

I'm thinking something with the action economy? so I know legendary actions are good fixes for that, but is there anything else?

Don't worry about lore reasoning and stuff! I got all that covered lol

and I'm not looking to just deny their powers, if I wanted that, as a DM I could just say "they win"

I guess I need to be more specific.

If you wanted to build a  single creature that has contingencies/strategies for each PC archetype (ways to counter melee tanks, archers, casters, sneakers) what feats/spells/preestablished abilities would you give them?

I was thinking for starters, giving them the "mage slayer" feat for casters, and some kind of access to spells that force INT saves since INT is a common dump stat for melee classes

You can use any monster to take down players, all that matters is your supply of monsters and opportunities. 

Strahd Zombies are a personal favorite of mine for various reasons, first of which being that they’re fast, get 3 attacks a round, and if one of them grapples a player, the rest of them get advantage on their attacks. 

Since zombies also like to wander around I enjoy putting them in multistory structures, that way when the fireball inevitably goes off, it brings the upper floor down with a fresh batch of slightly singed zombies to attack our grappled players.  

That one always works :)

Use other PC-types. Surely the emperor realizes how useful this type of person can be, and rather then killing them all, has kept a few alive and turned them into his agents. Maybe the agents even try to recruit the PCs to team emperor. If the PCs agree, well that changes the campaign. Either way the one who tried to recruit them becomes an ongoing NPC. Could be an enemy, could be the PCs try and get them to turn against the emperor.

The big property required for general purpose 'PC slayers' is the ability to identify PCs. I would be tempted to have 'PC' be a creature type, just like 'celestial' and 'fiend' and so on (or possibly actually assign PCs a creature type, meaning they are vulnerable to effects such as protection from evil and good), and have detection effects that work on them. Given that you're talking knights, I would be tempted to use paladins with Divine Sense replaced or augmented with the ability to detect PCs.

Essentially you're really just talking about a creature that has a CR rating substantially higher than the PCs. From what you describe, Inquisitors should be really scary and you'll have the PCs choose to run from them from say levels 1-4, and perhaps take one on at level 5 with a chance of winning at the first time? If so, I'd keep things really simple. Give them a strong stat block and an iconic way of dealing damage, for instance they use psychic fists or something.

One alternative that might be fun... give them this Reaction ability:

Replicate. When the Inquisitor observes a Hero using a spell or class ability within 100 feet, the Inquisitor instantly (but temporarily) learns the spell or ability for 1 minute, after which it is forgotten. The Inquisitor may use a Bonus Action on any of its next 10 turns to mirror the ability. If the ability targeted the Hero using it (e.g. Wildshape, Action Surge) then the target is the Inquisitor. The Inquisitor may observe and be prepared to use multiple different abilities, and can only replicate an ability one time, after which it forgets it again.

To make this fun?

I would create a great deal of one-use magical items which affect the heroes, such as antimagic nets (activate and they last for 1 minute, then they're just nets), for example. Then, I would equip these items to guards.

You want the players to feel above-average, so you don't want there to be people who are hard for them to deal with, you want people who are easy for them to deal with, but who are equipped with things which make them a threat. The god-emperor doesn't let heroes live, so no-one in his employ should be heroic, they should be average-joes with cool gear.

Look at any scene in a superhero film where the henchmen try to take on the hero. They swarm them, and yet the hero beats them all up and is made to feel powerful by doing so. Having the party pursued by normal people with fancy gadgets and magic items (which are limited use so that when the players get them they don't become OP, or which are powered by magical glyphs branded into the task force so only they can use them - I like this idea a lot, now I've come up with it!) will make them feel awesome tha tthey're taking them out with one punch/spell, but they keep coming. Far more fun than if they find themselves slogging it out, and thinking "and they think we're the threat?".

If you want to cripple a mage, cast Silence, Darkness, or Blindness/Deafness. Nearly all spells require a verbal component (impossible in a Silence field), or require sight to target a creature (which Darkness or Blindness will take care of in most circumstances). Also, a martial character would be attacking at disadvantage if they were blind, unless they have Blind Fighting. 

I agree that limited resource gadgets, scrolls, or potions is the way to go, since it would be insanely frustrating as a player to go up against this every single time. Nobody enjoys getting the tar kicked out of them on the regular. Maybe the Inquisitors have like a beefed-up Darkness Grenade they throw as crowd control, and all the higher-ups in the organization have Devil's Sight or potions of Truesight so they aren't impaired. I think it could be cool if the average citizen knows Inquisitors are capable of crazy feats like blotting out the sun - builds up hype for the eventual run-ins with these "legendary" hero-slayer knights and gives the players hints about how they might combat them. Besides, who doesn't like a good Boogeyman?

Also, for what it's worth, I'm going to be playing a sorcerer in a campaign where arcane magic is illegal, so I think the idea of having heroes be hunted for who they are is a fun conceit if you have the player buy-in. Good luck!

I suggest various levels of Star Spawn or Core Spawn.  Really unique enemies and very novel ways of attacking.  Really alien-like stuff. 

Even without anything special, a squad of human “monsters” with a CR equal to the PCs level will threaten any party. Especially since one member of that squad by itself will theoretically challenge the party.