I like the level in R Type where you fly around a giant ship, blowing pieces off, so I put a boss encounter like that in AstroShift. He has a shield up, so first you have to fly around and destroy the shield generators. Then you can blow off pieces of the hull, exposing the important bits underneath.
I put in touches like: if you destroy the engines first, the ship slows to a crawl, making it easier to fly around it; if you destroy the control computers at the front, it will stop sending out fighters to harass you, etc.
These aren't spelled out in the game, but they are there to be discovered