1) i agree, at the moment they just go slightly darker for 2 frames
2) agree
3) weapons are definitely not underpowered, you can reach OHKO range on many of them quickly with the upgrade and damage system. They start off fairly mediocre. The rocket explosions destroy walls on the third explosion, a visual indicator could definitely be used.
4) That boss acts kind of like jjba Dio, stopping time, and yeah it could definitely do with some more elements to it, like stage manipulation.
I'll try and scrounge some stuff together, but i havent really worked on this for many months so i cant make too many promises.