I do think that story is one of the things that suffered the most with the transition to the open-world, non-linear format. However, I think what you're looking for in Zelda is a narrative, and just because the "character" of Calamity Ganon is minimal doesn't mean it lacks impact or even importance. To clarify: you speak about "hating" Ganon in Twilight Princess because he's manipulated people that are close to you, and killed, or come close to killing, several people. Except the majority of the characters in Twilight Princess remain completely unscathed. Calamity Ganon has lost "his" humanity, if you can even assign gender to it, any longer. He is power incarnate, and he has done far worse than anything Twilight Princess Ganon has in his time. He kills four central figures in the narrative without mercy, whether or not you feel connected to them. He has unleashed the very Sheikah technology that was used to stop him on Hyrule and, in case you didn't hear any of the lore behind Hateno, wiped out most of civilization. The reason you have to regain control of the Divine Beasts and go to face him again is half because he wiped the floor with you 100 years ago, and half because Zelda was forced into a conflict that she was not prepared for.
Again, this is definitely a difference of opinion, but I never hated Twilight Princess Ganon, nor did I feel his reveal in the second half of the game was warranted at all. Zant was a more interesting villain in the first and second acts without Ganon being the puppet master, and then became a literal joke so that he could be swept away for the final confrontation, which was indeed dramatic, but really as a result of great aesthetics and music.
Now, that being said, I would agree that the fight against Calamity Ganon was disappointing, but for entirely different reasons. If I had known I would be taking off half of his health bar because of freeing the Divine Beasts, I never would have done so. I wanted to face this guy head-on and I expect that I will have a very different experience when Hard Mode rolls around, because, once again, I want a challenge. I also feel that, a 1v1 sword battle at the end of the game would have been a nice, intimate way of finishing things out, and that there should have been a third phase to the boss. As it stands, the climb to Hyrule Castle is harder than the final battle, which is pretty sad, and the final battle just doesn't ask as much preparation of the player as I had hoped. I still enjoyed the parallels that final sequence had with earlier fights in the story, where you had to disable the Divine Beasts before entering them.