Thanks for playing!
The game is not perfect by any means. There could be many more systems working in the background to help the player in invisible ways. A fully charged shot takes out 10% of boss health in 4/6 bosses that are in game, I think that is a fair amount. It could be flashier, I agree.
Patience and chip damage is also rewarded in the long run. Better to shoot 1st or 2nd charged bullet then none at all, if there's an opportunity.