I'd actually like swimming to just be a basic skill of Link's. There's no logical reason why Link shouldn't be able to swim like he could while wearing the Zora Armor from Twilight Princess. Since Skyward Sword Link can run now, and has that stamina meter built in, I think a natural swimming ability without water-breathing would be awesome, and while underwater stamina could become your air supply. They can still add in upgrades to your underwater abilities later in the games, such as weight to sink to the bottom, water-breathing, or fast swimming like the Zora in Majora's Mask. I would still like to see armors or other equipment with special powers, so I wouldn't mind that.
I like the idea of it working like that, and because of the presence of the running and the stamina meter, I think it's a legitimate possibility. At the same time, because of Skyward Sword's placement at the beginning of the timeline and its trend of having classic enemies from the old 2D games (well, so far as we've seen), it's also somewhat likely we'll just have something classic like the Flippers return, and that will be the item that allows Link to swim at all. I don't know. I would prefer the basic ability to swim. :bleh: