Scaling is a big issue. I marked two areas in the pixel version and the ref where the scaling problem reveals itself the most. See how the guy in the back should not exceed the planes snout in height and how the one in front of the plane barely reaches past half the snouts height. The third area I marked contains invented detail which is not there in the ref, I think at that angle we see much less of the wing attaching to the trunk. It might be useful to check
other references of that plane type to help with placement. The wing definitely should not attach that close to the hatch.
Also, it seems you made the whole bottom of the plane almost completely horizontal when it actually rises to the left much like the top does, so that the snout should be higher and hide more of that building in the far back.
If you are having difficulties freely eyeballing the ref and getting the scale right, I suggest just tracing over a shrunk photo to get it right before starting to render any detail, light or shadow.
For the contrast problem on the plane, I would start by shading the entire plane in the darkest blue first and then adding the light from the top, perhaps as just a 1px wide line along the contour. Maybe that would suffice to have those two different colors with minimal AA to replicate the effect at this low resolution and omitting the smooth transitions we see in the ref entirely (or just have one additional tint for that).
All that being said though, I think an even better approach for something like this would be to NOT try to replicate the ref closely like a pixel painting and instead pixel the scene and all objects in them in a PixelArt/Gamey representation with an eye level and camera angle(and parallel projection) which lends itself better to the low resolution (think classic "Street Fighter II Guile Stage") because more angles then can be aligned with more pixel art compatible line angles.
