You had everything right, EXCEPT!
You need to change one thing. Either have an upgrade menu for your ship. Or the upgrades you get from the enemies are permanent.
I got very annoyed with the whole "upgrade" system
I was like "YUS" when I got an upgrade, then it just went away, I was like "WTF!"
It was seriously lame.
BUT other then that.. the game was allgoods.. I guess.