I hope you do add Dive areas. They're very appropriate for a region with so much water, and they make the ocean feel more 3D.
Glad you got the Pinkan Berry working. And the battle with Tracy looks fun. He's a recurring character, right?
Getting Lapras early on is a good idea, if you want an exploration-based game. If you think Surf is too powerful to have that early, you could make it weaker (60 power?), which would also encourage the player to use more diverse Water moves like Scald or Brine (if you add them). Or have a ferry between the first two or three islands, so they can get Surf later.
The GSC-style Cut tree stands out among the other new tropical plants. What do you think of these from RSE or FRLG? Or maybe use a different plant entirely; a coconut tree, or a different kind of vine.
More graphical nitpicking: there's nothing wrong with GSC's quad buoys, but I personally like the rocks from Pokémon Christmas. Just my two cents. Maybe have buoys around inhabited islands only?
Also, larger whirlpools would look pretty cool. Here are the ones from
Pokémon Pinball RS, looking similar to the HGSS ones:
Picking four of the five frames, they can sync with the 8-frame water animation either at half the speed:
or by repeating twice: