I think the angle on the ship is looking pretty decent. It might just seem weird because everything else is pure isometric, but logically it works. Particularly if you add objects later that aren't at the pure isometric angle (if that makes sense).
Other thoughts:
1) The grass is way too busy. The intense detail distracts from everything else that has larger pixel clusters. In general the scale just doesn't work, because it looks like grass with little doll houses.
2) The outline on the ship is way darker and harsher than everything else. Maybe you are doing it to make it stand out more, and maybe it looks better in motion during gameplay.
3) Is that shadow bigger than the ship? That isn't how shadows from the sun work, it is impossible for it to bigger (right?), particularly if you are trying to convey that it has distance from the ground.