When I look at the image, there are a number of things that jump out at me:
1. The rain clouds look too blue; certainly where I live the only time we see clouds like this might be during a thunderstorm during the latter part of golden hour. Normally they tend to be more gray;
2. The line where sea and sky meet looks strange (as you have pointed out); and
3. I don't like the boats on the horizon line; I find them a bit disruptive to the view.
What I did in my edit is to reduce the blue/cyan component in the rain cloud to give them a more neutral colour. I cloned out the small boats and I cloned out the dark line between sea and sky. I also applied a slight vignette to the image, one that is just barely noticeable.
It's not a perfect job, but you should get the idea.