They're both excellent games to me; I can't decide between the two.
I look at various aspects of any game instead of considering one to be over another by default. Nevertheless, I do make exceptions depending on how gross the "negatives" are, negatives like the sailing in Wind Waker, which hampered my enjoyment. This is not the case with Skyward Sword and Twilight Princess. They both contained enormous facets, such as character development and poignant moments, and these outweighed certain repetitious occurrences. Although I consider those to be more notable in Skyward Sword. All the Imprisoned battles and Silent Realm incursions were trifles in the face of the overall adventure. I utterly enjoyed sporting the Wiimote as if it was my blade. Motion controls are something I'd like to see more of because it ended up working well; even so, I want to return to button-mashing one day.
Twilight Princess is tremendous as well, but I feel it's egregiously under-appreciated. It matches up to Skyward Sword's level almost perfectly. To me, both titles are no more than coequals. Fi's over-enlightenment and Midna's pushiness might've chagrined me at first, but delving beyond the surface of the game takes you to a beauty buried deep within. It's something that touches you as you move on through the game, working to solve a character's problem or warding off a band of enemies intending harm. This...magical feeling has affected me the most in these games, and Majora's Mask. Due to the tempo of this series' formula, especially in the aforementioned installments, I relate to the struggles Nintendo incorporated into them, as any human would in real life.
I couldn't say it better myself.
