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.