If you're going to replace entire parts of the map, you could draw your own to begin with, couldn't you?
It's more than enough work to put a map together. Adding extensive Photoshop work to the process will only make one thing certain: That it doesn't happen.
Maybe you're right, and having done this for years, I trust your opinion.
But the thing is, considering all elements a map must have (considering battlemaster), the water effects are really the minor part. The only parts of the maps in which what happens in the water is of significance are some sea routes, and they can easily be made as a mask over the water, with perhaps a boat drawn there.
Of course, the amount of photoshop work depends on how perfect you want water effects to be, but depending on the awesomeness of the map editor, I wouldn't mind water being solid blue, if that's what it takes.
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On another approach to this problem, the large scale maps that show the whole world could be made as actual maps, different from the region(/duchy/realm?) views, which could have the artwork from the civ5 editor, because they could be done in a single screenshot.
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Other than these, let's keep looking for a good map editor.
