Yeah they should be bright but that's not the only thing, right now a lot of enemies aren't too much bigger than bullets or random debris, and the colors themselves don't stand out TOO much from the bg. During normal gameplay it's not a big issue but once you get a huge loadout and start seeing bullets ricocheting all over the place, or are focusing your eyes on boss attacks it can be very easy to miss enemies. I'm not sure there's a very clean solution to this besides maybe something sloppy looking like outlines/auras, or redoing enemy designs to make them bulkier so they're more clearly visible in the heat of the action. Nex Machina is probably a good reference since it's a very visually busy game that has no problems with visibility.
Regarding the loadouts, I'm spitballing but maybe make the player lose upgrades one at a time instead of all at once if the time limit runs out, while lowering the extra time gain from picking up extra upgrades? Potentially that could add more pressure & challenge forcing the player to be smarter about timing pickups, without being overly punishing. Being overpowered is cool, but I feel like it's good to make the player work to sustain that OP state a bit