Okay this is just my opinion, but many people think Zero and Yuki was pretty unexpected or just a last minute thing Hino put in. However Yuki went with Kaname for a year and she was unhappy and awkward with him. In contrast she could be herself with Zero. Whereas with Kaname she was reserved and shy, even after a FULL YEAR. With Zero she was back to her past mannerisms with him within a couple of days, even after not seeing him for a year. Not only that but she knew that even though he had been hostile upon finding out she was a vampire he didn’t mean what he had said about wanting to kill her. They understood each other in a way no one else could. Ultimately I think that’s the message of the story. Infatuation is one thing, but love is another. Love is accepting someone for who they are and not for who you want them to be. Kaname was infatuated with Yuki but he never really took time to know who she really was. He was still in love with the hooded woman and in the end couldn’t really get past that. Yuki was a prize to Kaname, but a partner and equal to Zero.