(second part of my comment)
3) I am a very big fan of games with auto-money collect, but the money still looks kinda too much like bullets. But that's only a minor issue now, it got way better.
4) You are aware that you have a very exploitable bug there with making every enemy worth the same money, right? Farming by getting yourself killed by the first boss is very easy to avoid difficulty in the later game and since your bullets don't spread out much it's also very possible to farm the second boss and the homing missiles it spreads. Hard mode is a joke if you upgrade fully before going into the third stage. Different money values are definitely a must!
(Two posts because there is a character limit, lawl)
The Good: Very good difficulty curve, very nice bullet patterns, good control over the ship, hitbox is good and I like the purity of it all. It's not too difficult, but challenging and you get bonus points for having mouse controls available. A very enjoyable game overall, but there is room for some improvements.
Suggestions:
1) Good lord, what made you think that making the homing stuff the most damaging thing in the game was a good idea? If you get hit by the two things the third boss spawns (which almost always happens if you get hit), you die at once if you have 50HP. It's hard enough to dodge them anyway since they have such sudden movements and there are lots of other bullets to dodge.
2) Why is there no save function? =(
 "Pixel Warrior"){kind=icon}