He'll end up with Ai. They've been through so many things together, and they understand each other without having to say a thing. Also, Ai deserves a happy ending. They should just grow up together, and THEN they're going to be a childhood couple. Perfect.
She's just used to having nothing, so she doesn't expect him to love her back. And what's wrong with her wishing him happiness because he's the one she adores? :/ She thinks Ran can make him happy, so she wants them to end up together. Simple. ...She protects Ran because Ran reminds her of her sister. I don't think this has anything to do with Conan (helping him protect her or sth).