Are you making the enemies stronger based on how many upgrades the player has purchased? If so, that makes it harder and harder to earn money and kind of takes the fun out of it, especially when the upgrades (except for damage) tend to be very small improvements (+0.02 per upgrade when the starting fire rate is 0.5, +1% chance per upgrade for the special bullets). It would be like indiscriminately jacking up prices based on how many times a player has prestiged, in a traditional incremental
Ah, then this is something you must make clear to the player, because up until the 2nd run it just looks like a shooter with Arkanoid elements and purchasable upgrades.
While I appreciate you're bringing your own flavor and uniqueness to the genre, you should make sure players aren't caught off guard because they're expecting a conventional roguelite experience.
Maybe add a "refund upgrades" option so players with poor builds (like me because I was surprised by the adaptive difficulty) don't have to wipe their save?