The upgrade system is really nice, lots of fun to gradually become more powerful, and the effects felt noticeable, especially the one for number of bullets.
One suggestion I have would be to avoid cases where the positive and negative effect on an option counter each other directly. For example, having player attack damage go up but enemy health also go up is essentially no change.
I also felt the color shielding mechanic was a bit unnecessary and took away from the cohesive identity of the game. It didn't negatively impact my experience since it wasn't explicitly required that you use it, but I just thought it was a case where the added complexity didn't necessarily contribute much to my experience.
Nice work overall! I had fun :)