I really like the stamina system, but I think it should be used not as a clock but as a turn counter. Maybe instead of losing stamina based on time you would lose it based on how many attacks you do or how many attacks you block. Then, you could add more debuffs like fatigue, which makes you lose more stamina per attack.
Also, the enemies should scale more exponentially instead of linearly, as the game doesn't increase in difficulty after the 5th stage
Other than that, great game!
Choosing what to do would be a great idea!
It makes the combat more tactful, and you could attach different statistics (the straight up damage and defense combat is really boring) to different actions. Maybe after a boss, instead of having another shop, you could add a way to upgrade your actions, and in normal shops, you would only have options to heal health and stamina. This also helps with the scaling problem as you only get stronger at 1/3 the rate. I don't know what you will do for the gems after a run, as currently they just make you start out stronger, but I'm looking forward to it!
