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.
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.