I played around with your Capx, fixing a few glitches. I think I fixed to a playable state, but don't save it over your other one, in case I did something you don't like.
https://dl.dropboxusercontent.com/u/85412219/forumposts/FixedSpaceGame.capx
There are Comments with things I did.
Edit: If you'd rather I didn't leave your game source up, let me know and I'll delete it.
In case someone is also looking for similar answers, mainly what I did was change all ships to face right in the Animation editor, because all behaviors expect the front to be to the right, if your sprite isn't it will look funny. (Except the boss ship, which just slides side to side.)
I set the boss bullets to aim at the location of the player, so don't sit still. (I didn't beat him after that.)
I also fixed image points, for example the star animation had a bounce in it due to a misaligned origin point.
And I set it to rotate one ship sprite so it's direction could tell the bullet where to go. (rather than using sprites facing each direction.)
The different animations can still be used, as long as they all face right.