Ok, I am going to say this now, that problem is incredibly overblown.
As someone who has played the original version MANY times. That has never been an issue for me. Why? Because I always pause the game and change the batteries after the first time she says it. A good pair of AA batteries should last you a good 15-20 hours. One playthrough of Skyward Sword is usually around 30-40 hours, depending on how many side quests you do. So, you should only really hear it around 2-3 times a playthrough (Oh, the agony!). It's only a problem if you constantly ignore her and keep trucking on through playthrough to try to squeeze out every ounce of juice those batteries have, in which case, I'm sorry, that's not the game's problem, that's on you.
Sorry, man, just love to be the funny dude. As the mapache said, I just said it because that's how Fi's usual perception goes, she constantly interrupts you, and while she does have cute moments as the one you posted, all of which amused me when I played the game back in 2011, those are a rarity.
My bet with The_Liquid_Laser: I think the Switch won't surpass the PS2 as the best selling system of all time. If it does, I'll play a game of a list that The_Liquid_Laser will provide, I will have to play it for 50 hours or complete it, whatever comes first.