The story in pretty much every Zelda games is way to shallow to get much emotional impact from me. Skyward Sword was no exception. If anything Majora's Mask had way more tearjerkers
While I can tear up quite easily with series and movies, Games in general havn't had that much impact on me. The only one I can remember was Mother 3, that got me good.
The first time through, I started feeling slightly emotional at Fi’s goodbye. Her whole “I’m gonna say something we’ve heard from people over our journey. Thank you” bit got to me.
Of course, I quickly realized it had no depth because it implied Fi experienced development (she hadn’t) or that you had been making deep connections with the world throughout the game (you don’t). If Fi was a bit more interesting and you actually interacted with several interesting characters, then this scene would actually be good.