I'm sorry, but in my eyes this statement is fallacious. Twilight Princess is a good game and a superb Zelda title. I can't decide between it or Majora's Mask (and now Skyward Sword, which I finished today). TP is just too epic for either title to overtake it. Midna is a huge contributory force to me liking nearly the most. Many people don't like her character, but she was meant to be bossy and conceited early on. But the further she with Link went into their journey, and the more she saw of the Light World's suffering, all that changed her. It's not her, but the level of the player's in/tolerance in this matter.
Getting back on track, Twilight Princess excelled in so many areas. Some moment of Skyward Sword seemed to stir up the same sentiments that I experienced during several quests in TP. Ilia's amnesia played was a very impacting element in the plot. I was astounded at how immaculately touching the reunion, and even sequences beforehand, were. Though Ganondorf's presence was only felt about halfway through the game, we still got to see he was the reason a pall of twilight descended over Hyrule to begin with. That justifies well enough his appearance, however sudden.
I could go on and on about this, but the issue is only to me as big as the amount I've let spill out above. Arguing it is quite trivial as I doubt it'd persuade anyone elsewise. Not that it was ever my aim.