I love the idea of building up your "deck" and the longer-term strategic decisions involved. Some food for thought:
Perhaps you could progress by making upgrades to your shop that persist throughout your run. You would start with a very basic shop and could have upgrades like: Unlocking modifiers, discounts, improving symbols/modifiers, locking shop entries, increasing the odds of certain modifiers appearing, increasing shop size, etc. You could also add persistent "artifacts" that give you bonuses to your die faces, rolls or abilities such as: Adjacency bonuses, modifiers for nth die face, debuff barrier, bonuses when rolling certain combinations of symbols, increased ability charges, ability gem discount when low health, etc. The score earned in a scenario could have a minor effect on the amount or quality of upgrades you can draft.
I think this would retain the core mechanics you mentioned while still allowing for incremental progress. With some careful balancing in this progression you might be able to avoid making drastic changes to the scenarios