My plan was to convert all shore combos to 'ladder only' and make only the open water combos swimmable (so the Ladder would still be viable in these situations, and without it the only way into the water is a raft pier). The addition of flippers exists primarily to hide more secret entrances in the water, and to ensure said entrances cannot be reached until the flippers are acquired.
If I could find or construct a script that would let Link move freely on water tiles when he has the raft (probably just needs to check for the item, then combo type, then draw the raft on layer 0), the flippers will no longer be necessary.