the approach to the lighting will dramatically effect how flat your ship looks, if the light you want to apply to the ship is a form of overlay filtering that alters the existing colours, then it might look okay, but if it's just a simple lighten overlay it'll reinforce the flatness, I could elaborate more but hopefully you know what i mean.
and regarding your ship shading, you should avoid having so much banded clusters, here I'll just highlight some

red=
some of most noticeable cases of pixel banding, green is where you have applied some forms of combating it, but the yellow is showing the banding still present, banding is unavoidable especially at this resolution, so I must say do not avoid it entirely it'll just wrack your brain, but try to minimise it for sure, something you shouldn't be afraid to do is push the highlight tone to the dark tones, buffering them with the intermediate tone is not always necessary and alot of the time just causes banding. some of the things in this edit are effective

ignore alot of the redesign, just some experiment but hopefully some of it is useful, I think the balance of details on your original design look effect in the rotated example, so maybe pushing some of it back to that, most notably the grey wing tips look good and could double as the origin of the lasers/blasts etc (the guns) and the light yellow features on the wing serve well to reinforce the orientation of the ship, the latest one they don't stand out so much, also a possible approach to lighting when the thrusters are active having a sprite change, maybe even 2 or so frame light flicker animation.
you're meteors need work, I'm sure the forum will offer ample help if you get around to refining them and ask for feedback