Cool, so it is just quite low Fov.

I would add to eishiya's list that the ship's green "windshield" (don't know the equivalent term for airplanes and ships) have gradients that look a little too smooth for typical pixel art, and it seems to be skipping the dithering part of the style (intended?).

Anyway, this looks really great . If I were you, I would be tempted to rebrand this as a game without WC IP/designs after you are finished having fun . Also, do you have any plans on commercially releasing your pixel-art rendering tech as a shader?

Lovely stuff, i like that it is a bit like master blaster and you have separate sprites for the vehicle and the pilot. The only two things I can think of is:
1- I am not so found of non outlined sprites, but as you are having dark backgrounds this is probably the best choice.
2- perhaps you could unify the tint of the big objects shading towards the dark blue/teal of the background for more ambience (like you are already doing with the green paint parts). Going more realistically underwater than that would mean filtering the red element of colors, and I don't think that would improve anything, as the lively oranges and red mid tones are looking nice, so maybe just making the shading globally colder would be a good compromise.

One relevant question is the ratio of your tiles, are they 1:1 or is there any foreshortening on the y axis due to the view (4:3, 2:1)? If so, I think you latter version is better because the side waves are shorter than width of the top waves. Even if the tiles are 1:1 the vertical shortening would be a good stylistic choice I think.

Also, are you going to put any classic watery texture on the surface, or going for plain color blue like Zelda with ocasional breaks? I wonder how a jrpg watery texture would interact with animated wavy borders like yours.

Excellent object of study, and good choice of starting simple, narrowing it down to the essential.

Thanks Meat! I wasn't sure about the part where the blades glint when rotating out.
Now this one is should be so simple that it is embarrassing, but I am clueless. It is just a spring tile, sonic style, but as you can see the movement is linear. How on earth do you figure how many frames to duplicate, and where to duplicate them, in order make it sine-like as a spring?