Very interesting choice of genre combination. I'm not entirely on board with how the combat works though. What if instead of two separate games (the top down shooter outside the ship and tower defense inside), the aim of the game was to board enemy ships with raiders while they do the same to you? That way there would be more cohesion between the two distinct elements and would open up the possibility for a variety of play styles (do you prioritize interior defense, or are you going to focus on destroying the raiders before they can board?). Currently there's not much choice, you always have to focus on the interior a certain amount, or else you lose.
It's still a pretty well made game, I just think it could be developed into something much bigger, maybe sometime after the jam.