I do quite like the concept. Backtracking in games is something that I can enjoy when its set up correctly, and this game does it right.
I think that the checkpoint system is a big drawback here. It's good to have well-defined checkpoints, but be sure that they are everywhere they're needed, and that the player knows where they are and whether they have actually saved.
I also noticed that if you go into a hazard meant for the ship while outside of the ship, the game will respawn you back at the nearest checkpoint in front of an out-of-ship platforming section. You probably want to make sure that both checkpoints are executing the same code, if that makes sense.