I kind of want to see a crawl, walk, run approach used with underwater exploration. I somewhat agree with
Asbsand about it being somewhat tedious being a strength, at least for a bit. Though creating any kind of progression is admittedly hard to do in a open air game without any kind of linearity, but there is value in limiting how quickly we have access to something.
Being able to dive and swim around for a limited amount of time underwater, then getting something like the Iron Boots that lets us actually walk underwater and interact with certain objects and then acquiring something like a Zora Scale that lets us breath underwater and swim faster is a nice progression. This could work in a game like BotW by not explicitly gating anything off from the player, but by simply providing less efficient alternative means for players to replicate those abilities without said equipment.
So from the start we'd be able to dive and swim underwater for a limited time, and while the Iron Boots and Zora Scale might be something we have to find, they aren't items we need. They would just be the most efficient and convenient ways of providing those abilities. We could make a potion or dish with something like Ironshrooms that makes us heavy for X minutes and effectively have Iron Boot abilities to walk underwater that way. A Hasty dish could help us swim faster. And maybe a new dish effect could help us hold our breath for longer. So players wouldn't necessarily be locked out of these areas, just they would have to prepare and do more in order to access them without the recommended equipment.
I would like for them to use this approach to a number of aspects of the game in order to reintroduce certain items as well as craft a technically linear story path through the game, while not actually limiting or forcing players down it. Similar to other open world games where you have the main story path, with certain events and rewards, but you can choose to engage or ignore it as you like and explore and do anything else in the world should you choose to. BotW already did this in a very basic and loose way with it's main quests of pointing you to Kakariko Village, gathering the memories and investigating the Divine Beasts. It would be similar to that but a bit more fleshed out.