I saw the health potion, it's a must buy!
Upgrading the chest seams a great idea and would allow the player to specialize its gameplay towards what he likes the most. One could specialize in rats while playing the piper class by buying all rats related upgrades. The same goes for chests, the player strategy could circle around the concept of upgrading chests and finding them as soon as possible via tarot cards and the such.
You are right about the shop. There's no hint to it and most player might not even experience it, which is a shame. Chests could give the player an anticipation for what's to come, thus motivating the player and keep them engaged, but I feel like this is not enough. A possible Idea, enter the gungeon approach: you let the player know beforehand that more items can be unlocked via the shop or after each game spending some kind of acquired currency. This way you build curiosity in them. So, initially, chests provide only a small catalogue of possible drops, but after reaching the shop you can not only buy an item, but that item might spawn from a chest in later levels/games. This is more of a roguelite approach, while your game is more roguelike oriented, so it might not be the direction you want to take.
The different biomes idea sounds interesting. This gives me another idea. You know when in games there are entities that not only damage the player but other enemies as well? Like carnivorous plants that eat whatever comes close to them? It makes you feel like you are part of something bigger. It might be that it is actually beneficial to keep an enemy alive for some time (eg. you have a poisonous fly enemy 3, and a carivorous plant 5. While the carnivorous plant is alive, nearby poisonous fly enemies have their exp/life reduced by 2) Enemies interact with each other in an antagonistic way. Food for toughts