Cool game! Really liked the core gameplay loop. I will give my own thoughts on possible additional features to spice it up since I see a lot of potential:
The lack of variation/progression in the map was a problem. Enemies should meaningfully scale with player power so the game doesn't get boring as it gets easier. If you are worried about enemies outscaling the player just make the difficulty increase optional ex. poe2 map mods. Allows for a more satisfying difficulty curve without much more work.
Making lategame soul gated is kinda lame because you don't get them from killing enemies, so you just load into the map, run around and get souls, and leave. It should really be the opposite, early game should require more mats which are easier to get while late game should require more mats that enemies drop.
Enemies do too little damage. In a game like this it'd be fair for a melee character to do 1/3 of your health and a ranged to do maybe 1/5. Health felt useless and I was literally intentionally tanking like 5 enemies at once because I knew they couldn't kill me. For context I didn't die or fail to extract a single time the whole game.
Kronii's attacks are just way too fast to avoid. I beat her first try with fairly minimal upgrades by just standing still on the portal and whaling on her because trying to dodge her attacks is a waste of time. Just decrease the projectile speed 5x and increase the number of projectiles by 10x and it'd be a proper bullet hell fight.
You could try and make upgrades a bit more interesting. Some simple options I can think of are: multiple projectileinstead of just one, penetration of more than one enemy, crits, lifesteal, But I don't have a big complaint honestly, the skill tree is fine for a game of this scope, if anything it's a little too big.
Overall I still had a lot of fun though, good job!