One of the major breakaways from traditional Zelda gameplay in BotW was how Link only got a few Runes to play with and no permanent gear or key items (aside from the completely missable Master Sword).
Despite their absence, it was pretty difficult to miss the Hookshot and various magical sticks Link's used over the years because the Runes are put to such good use. That doesn't mean it has to stay that way, though.
Aonuma mentioned the goal for the Breath of the Wild sequel is building on the world that was already established with the first game. That's a pretty open-ended statement that leaves all kinds of things to the imagination, like more obstacles in the overworld, more puzzles (see Dungeon slide), and generally more ways for Link to interact with the world.
Relegating some items like the hammer and boomerang to normal weapon status and then basically replacing the Hookshot with Magnesis (sort of) would make key items rather redundant — unless we got a whole new set of items. Or a whole new set of Runes to let players experience the game in yet another completely new and malleable way.
All of Hyrule's many high places and open spaces would lend themselves naturally to a Rune like the Cane of Somaria from Oracle of Ages as well, granting the option to make blocks or platforms, maybe even moving platforms.
But there's something even more important:
Zelda has magic, Link's controlled the weather before, and the rain sucks.
Put it all together and you've got a desperate need for a Rune that gives the power to control the weather. It wouldn't have to be limited to rain, either.
Giving the option to create a storm and control lightning, at a cost, would help vary combat options a lot. Plus you could save time by not dying when caught in a thunderstorm, or it could even be used to open doors or solve puzzles. Egads!