Great to see Anim8or being used for a serious project, nice work! There are a few things you can do to improve the quality of the animation, bearing in mind that some will affect render times:
1) In some places it looks almost as if parts of the ship's superstructure are lit from below rather than above. If you have an overhead light modeling the sun then you may want to check your normals are correct.
2) The lighting appears flat as if some surfaces are emissive rather than illuminated. Consider having a single overhead shadow-casting distant light as the sun with a bright-ish ambient light level, and ensure the ship model is set to both cast and receive shadows. This will increase render times but will improve the realism of the scene greatly.
3) Animated water is going to be very tricky no matter how you do it. Rather than attempting to animate actual waves I would try using bump and trans maps to simulate the effect of waves. I have had a bit of a quick go at this in the videos below (excuse the very rough ship model, it was a quick job for demo purposes only).
There are three large, square planes in the scene at the water level, as follows:
Planes 1 and 2: material uses bump and trans maps with a wave-like texture, each at a different UV scale and rotation for 'randomness'. They are on the exact same level (Y dimension) in the scene and are animated to each slide slowly in different directions (+X and -X respectively).
Plane 3 uses a partially-transparent deep-aqua colour to simulate depth, visible through the transparant parts of planes 1 and 2 as defined by their trans maps. The slight transparency allows the ship to be dimly visible beneath the water.
The an8 file and associated textures are attached, feel free to download and fiddle with the settings, particularly for the water materials. A lower Roughness figure may improve the wave-top highlights but this will also be very dependent on the 'sun' light's angle relative to the camera. You might also be able to find a better water bump-map online.
I would also suggest perhaps using bigger, circular planes rather than squares to give a better horizon line, and perhaps they could be rotating against each other rather than sliding (though this would create a centre point that might look odd).
This was rendered with Scanline so shadows could be less than 100% without the need to add more 'fill' lights, using the ART renderer would allow the surface of the water to be reflective which could add to the realism significantly but at the expense of render speed. Experimentation is the key here
Regarding the 'great wake' left behind, this would be really tricky in Anim8or. Without animatable material parameters (eg. transparency or alpha) it would be difficult to simulate this effectively. Something to ponder on...
