I agree with Daniel. Upgrade system is too complex and fiddly. Way too much clicking and options.
My biggest suggestion: I think the upgrade tree needs to have a "Buy whole cycle" button. For example, if I have 100,000 credits but haven't upgraded Multishot at all, I shouldn't have to click 16 times to get all the upgrades for one cycle to unlock the next cycle... where I then need to click 16 times, etc. Definitely needs a button to just buy the whole cycle.
I also got to the point where the screen is clear and I'm just killing enemies off screen. Upgrading anything seems redundant at this point. Maybe scale the enemies harder and move some upgrades into permanent upgrades for future runs. Makes it more of an incremental, but once you're killing everything without seeing it, the game ends when I'm only at 24/480 skill constellations finished.