I know that Fi has been considered more annoying than helpful--but I think Link meant that she is more than just a weapon. It can be seen clearly that Fi has become a close friend to Link here. So cute!
In my opinion the ending to Skyward Sword (in regard to Fi) was extremely sad. She was my favorite character. The ONLY way Nintendo could have topped it was if Nintendo slowly showed Fi becoming more and more human emotionally and verbally. That way when she dawns the infinite slumber, she will truly be missed. I wanted her more as a companion character rather than a walking probability machine.