Thanks everyone. @Erick_Howard & @Yee you are both correct that I didn’t bake the lighting. Still on the list of things to learn how to do.
I agree with you about the perspective obstacles Yee, I kept trying to find a way to make it not so difficult to see where they were in relation to the ship, hence all the lights on them. If I come back to this project I think I’ll totally rework the levels and make everything move on the x and y much more like a traditional side perspective game.
The thing I really like is the feel of the ship, I think it would be awesome to move around the overworld in the ship and then get out and go in places to explore on foot.
edit I went back in and changed the perspective to orthographic and reworked the levels to work without perspective obstacles, and I baked the lighting. Much better now.
Thanks for the suggestions.
Thanks everyone