I played a lot of M:tG at various times in my life, and games like Magic teach you a lot about these concepts. I would have never thought about it has I not had that experience! No shame in learning about the meta game!
It's also interesting that there are deck-building games which remove deck-thinning as as strategy e.g. in mystic vale your deck has a fixed number of cards, you can only fill advancement slots in your base deck[0], and you can't remove advancements. You can also acquire "permanents" (the vale cards).
[0] every card has 0~1 slots filled from the base deck, and position matter, you can't put two advancements in slot 2 of a card
There's a couple of reasons you might want to hang on to them in Slay the Spire, depending on what events come up, but getting rid of them is pretty important in this game as well.
Even something as basic as all the cards costing energy to spend and you have only a certain amount of energy every turn (that can be increased by other methods), forcing you to prioritize what to play, as opposed to just playing everything you draw and only the order matters, like in most deckbuilders, changes the feel quite a bit.
They were able to take advantage of the video game concept (allowing cards to morph within an encounter and over the course of multiple encounters) and put it to good effect. Technically you could do that with a board game with stickers or something, but it's a lot more effective here, and only permanent for a run as opposed to forever.
That being said, they did take a ton of ideas from existing games. It just feels a lot more inventive than most deckbuilding games I've played, where most of them feel like some combination of Ascension and Dominion, with little to differentiate it.
Innate of course doesn't have a precedent in Dominion, since you don't keep your deck around between games. Ethereal could - there's no technical reason you couldn't print a Dominion card with text like, "During clean up, trash this card if you would discard it from your hand". I don't think there are any such cards, and I suspect they'd be generally worse in Dominion than Ethereal is in StS. Actually, having a deck of cards using in junking attacks with that text separate from ruins and curses might be interesting - curses that trash themselves, so you could hand them out a lot more aggressively without destabilizing the entire game.
Dominion's traveler cards were Donald X's attempt to make cards that change during the game, though of course Slay the Spire can push that idea much further.
Artifacts and States are a little bit like the Watcher's stances, but less deck-defining. You generally don't build a deck around having a particular artifact or state, but you can use them to get a little extra juice.
I agree, limiting your plays each turn (either with mana or dominion's limited actions) does a lot to change the texture of a game. The Ascension family of deckbuilders where you can just slam your whole hand down every turn tend to leave me underwhelmed.
I don't mean to rag on StS for being unoriginal, quite the opposite, it's great.
I was a little hyperbolic in saying that virtually all of its ideas come from existing physical games, but the core gameplay itself does not stray far from its inspirations. Most of the gameplay elements you listed are present in mechanically identical forms in pre-existing games where possible (obviously the game being digital allows for mechanics that physical cards do not). Innate, Retain, Ethereal, upgraded cards (ex Pirate Ship), cost reduction and stances all exist just between Dominion and Thunderstone.
Not to be too pedantic but, Dominion also has an action economy, its just all actions (until later expansions) cost 1 resource. Another deckbuilding game, Mage Knight, also has an advanced resource-to-use-cards system and now that I reflect on it is probably the closest game to StS.
I'm not trying to argue that StS is un-inventive, they did a very good job of bringing rogue-like elements and persistent upgrades into the deckbuilding genre and a VERY, VERY good job at adding an addictive "one more run" feeling to the genre.
Now you're really making me want to check out Mage Knight. I was curious about it before, but maybe I should finally pick up a copy.
I hope you like playing games solo or have a group of friends just as excited about Mage Knight as you because it is a lot of rules with instructions that only make it harder to learn.
It's really not that much more complex than StS but you have to keep track or rules and perform game tasks (like refilling shops and playing out enemy encounters) that the video game would perform for you.
That's really where digital games shine, tracking lots of small numbers, states, and actions which would be hell to do by hand. That's e.g. why hearthstone can have persistent damage while that'd be super annoying in MTG: you'd pretty much need a -0/-x die per creature which would get very old very fast.
They left when StS took off, and Netrunner has since been discontinued (although there's still an active fan-run Tournament scene with fan-published cards).