Regarding progression within a run: A resource, like gold, can help here, but it's not great for the current setup from an RP perspective. You could set up various types of shop keepers (nature summon cards, equipment blacksmith, card upgrades or extra lives, etc) with 3 semi-random items you can buy with gold at the campsites. It adds choices and excitement for the player (What can I unlock? Should I buy this now or wait? Is that thief guardian with extra generation but weaker attack worth it?)
You have to be able to almost instant back-track to a shopkeeper to make this work, and it still doesn't solve the issue of pick-one-of-three cards on victory gameplay.
i.e. you don't want to deal with a shop keeper after every room
The good part of adding a shop is that it forces valuation of the cards (gold cost), and you can write a function for random enemy summoners that scales them to where the player should be. Downside is this doesn't deal with synergy.
Part of the challenge for the current deck building is that you only reshuffle at the camp. So you have to add new cards between camps to do anything. If you reshuffle every room, you would need to stop mana carry-over, but purging cards from the deck becomes valuable
So paying increasing amounts of gold to purge cards from the deck can be an interesting shop keeper
e.g.: first purge costs 5, second is 15, third is 50, etc.
Bad part of reshuffle and starting a 3 mana is that 5 mana cards become less valuable.