Hello everyone,
I would like to throw in my two cents. Having a region solely based on water is a great idea! The water type is my favorite typing and Squirtle is my favorite pokemon. So I'm a little biased lol
Personally, I don't think you need to rework the type chart
https://pokemondb.net/type/dual - scroll to the dual water type section. As you can see from this chart resistances and weaknesses are still accounted for and balanced.
lind524's suggestion is interesting and should be explored
For example, adding in new terrain effects, moves that interact with others in different ways (using electricity after a move has flooded the area), new combination move (so that the player has to be cautious of the opponent could use the reaction from one of their own moves against them)... But that would involve a lot of changes to the core gameplay...
For example if the player is in a double dive battle and one mon uses an electric move (chinchou, lanturn), if the partner mon doesn't have volt absorb or is not immune to electricity then they would also receive damage since water conducts electricity.
For surface battles on top of water you could have a pokemon usage restriction like air/fly battles in Gen 6. So only water, flying, and mons that can swim (learn surf) can participate in the battle.
For battles under the water you could have "dive battles" where only water types are allowed to participate.
Exploration would be a great feature and the ruins from Gen 5 come to mind, not to mention Gen 3/ORAS. You could have treasure to collect and find - relics, plates, coins, shards, etc.(use there item icons instead of a generic pokeball in the overworld). You could have a "Treasure Hunter" as a NPC that requests certain items. You could have a "Dealer/Collector" that is in the market for rare items and requests the player to seek them out then pay you handsomely for it - refer to Gen 5. Instead of the itemfinder you could have the scanner (During my first playthrough of ORAS when I acquired this item that's what I thought it was used for, to locate the underwater items. It turned out to be wrong but, I thought that it was an interesting idea).
As for fishing. My preference is the random tile encounters (gen 1-gen 6). If the player uses a lure ball while fishing than the catch rate is increased - like current games. If you are just surfing than lure and dive balls would have a catch rate of a normal pokeball - like current games. You can keep the three rods or you could have one rod and multiple lures (old lure, great lure, and super lure). Each lure would have different encounters much like the rods do now. Also, you could add additional lures for catching certain mons in a particular body of water i.e. a marsh lure would be more effective in the swamp.
As for dive encounters. Mons can be seen in the overworld and interacted with to initiate battles. Also, seaweed and kelp, like in Gen 3/ORAS, could also act as "grass" for those random encounters. Using a dive ball underwater would increase the catch rate.
Pearls and big pearls would only be found in oyster/clam mons.
Gym leader idea: You could have a surfing race on the back of your surfer either against the gym leader themselves or against a gym trainer. Not sure how to implement it but, you could have a water gun target mini game as well where you would go up against the gym leader themselves or against a gym trainer. The player would have to win both of these in order to face the gym leader - refer to the Orange Island anime episodes with Cissy.
This is all that I have for the moment. I'll keep thinking on it and if I think of something else, I'll be sure to post it. Good luck with your game and let me know when you've completed it. I would love to play it!