There is no way I could choose between Kyo and Tohru. Both of their stories are amazing, and their story together is even more so. Tohru is so strong, from her personality to her role in the Sohma family. She is the hero of the story, but because she doesn't acknowledge this, or take advantage of it, many people look down on her and call her a weak character. I believe the opposite because Tohru has a way with people. She understands them, and yet she has her own faults that she has to overcome, but she doesn't let anything distract her from breaking the Sohma curse, and she accepts darkness by creating her own light. She builds a family of her own by showing the Sohmas the kindness and love that she has always wanted since her childhood. I would argue that Tohru is the strongest character of the series, with Kyo as a close second.
Kyo is practically bullied by all his relatives, except Shishou, his father figure, and Tohru of course. He lived in darkness under the shadow of the curse, his mother's death and Yuki's superiority in the Sohma family. Of all the Sohmas, Kyo has the most difficult life due to the curse, and it shows. Everyone in the zodiac literally calls him the cat, with Yuki calling him stupid cat and Shigure constantly calling him a moron. Because Yuki, the rat doesn't like the cat, most of the zodiac follow him and avoid Kyo unless they are picking on him. Kyo's ultimate challenge is his true form, which has never been accepted by the Sohmas, and even Shishou admits that he took Kyo in from pity. Kyo has a lot of obstacles to face, and without Tohru, he would never be able to face them. Once Kyo is accepted as he is, he changes. He opens up to people more, allows himself to make friends at school and he doesn't look down on himself as much as he did in his childhood.
Both Tohru and Kyo are lovable characters who rise above the most difficult circumstances in life and create a future of their own. Kyo gets past the stereotype of monster while Tohru gets past the stereotype of angel. They learn who they really are and overcome all the obstacles in their way. That is why both of them are my favorite characters.