Interesting concept and theme for your game. Problem is, and I know it can be complicated to foresee, but in top down shooting, you want the player to be able to aim while moving. Shooting (attacking) in the direction of the walk is only good for melee attack. I know it's a bit of a pain for the art (you have to have backward walk and stuff like that), but one easy way is to go around it in 2D is going for a 90 degree top down view like Hotline Miami. It's not as pretty, but it get the job done for a quick jam. Otherwise, you could still create a 2D top down isometric view in your spare time and use it latter. Top down shooter are quite versatile concept.
Anyway, good game overall !