Fi. As much as I hated Skyward Sword, I have to go with Fi. Navi I felt absolutely nothing for, the "guardian fairy" was just a title thrown on her to make it seem like she was worth something to the player. The "lol I'm leaving see ya" thing at the end of OoT without any explanation didn't help her either. Fi on the other hand, even though she had sort of a lame personality, at least HAD a personality. She was actually helpful too (a little too helpful, as some people have pointed out), unlike Navi, who, when I'm sitting in the Water Temple nearly losing my mind, just flits about my head.