I love the first two ideas. Running in the water is a bit weird :S There should be a different animation for when you go in the water.
And I LOVE the idea of being able to do actions in the water. One of my characters is supposed to be semi-aquatic. That would be awesome if she could lay at the bottom of a river or lake.
I'm indifferent about the bubbles from the nose. It would be a cool touch, but it's not on the top of my wishlist xD
And while I was thinking about this. I think it would be cool if, when you get to the bottom of a lake or river, instead of treading water just above the floor of the lake, you could actually stand on the bottom, and maybe even walk?