There are definitely some shared elements, though they aren’t really implemented in the same way.
The method of traversing the overworld, for instance, is vastly different by design. For the most part, the Great Sea is designed merely as a buffer between the game’s challenges. It’s pretty much filler between the games actual challenges (which sounds like a bad thing but it’s good to have some level of that in a game). Meanwhile in BotW’s Hyrule there’s a lot more emphasis placed on the overworld itself as one of the challenges to be overcome. It’s not a particularly well designed challenge, but I digress. I would compare it more to Skyrim than Windwaker.
Similarly, picking up your enemies weapons is also handled differently in both games. In BotW it’s used as the main method in which the player gets stronger, which is pretty standard open world fare. In Windwaker it’s more like an optional quirk in combat. You’re almost never required to do it and it rarely benefits you to do so. If anything, it’s more comparable to using magnesis to kill an enemy with a box that happened to be lying around.
I wouldn’t even really call using the potion shop in Windwaker “crafting.” I’d compare it more to collecting different items in Banjo Kazooie than anything else. The same could be said for the rest of the spoils. Skyward Sword’s crafting is far more comparable.