Though the plot gets convoluted along the way, I believe it does stay true to the mangaka's initial intentions. As for Yuki's identity
It is hinted back since the very beginning of the series, ie her first piece of memories. A five-year-old girl waking up in the snow with a strong vision of blood would only be either a vampire hunter or a vampire herself. But why is such young girl being chased in the middle of the snow? Her parents, vampires or hunters, logically will not bring their 5-year-old to whatever business they may have, be it blood-hunt or vampire-hunt, but most likely will leave her in the protection of home; thus, where she is being chased off to should be close to their house. Then again, she is literally in the middle of nowhere, which is not likely a home sweet home kind of place for hunters, since they tend to stay close to each other and close to the headquarters. Such remote and deserted place seems way more likely to be vampire's hideout. That's why, since the beginning, I always thought that Yuki was a vampire. Furthermore, along the way the author does drop many other hints, which I shall not present so that this post itself would not be too long and drag on like Vampire Knight itself.
And Kaname's string of reactions does seem to have a somewhat logical reasoning.
First he avenges Yuki and himself by killing off Rido, the mastermind and the murderer, by using many pawns such as Shizuka and Zero, and eliminating the council, whose corruption indirectly and inadvertently favored Rido's evil intentions. He then tries to re-establish order, but here again he is faced with Sara's intricate and cold-blooded plans (which are surprisingly alike to what happened ten thousand years ago) and other pureblood's playful murderous intent. Mindful of the past, he decides to go kill all purebloods then turns Yuki into a human. While following the plan, he realizes the limit that the furnace is reaching, so he puts the killing on an indefinite hold and sacrifices himself to finish her will and succeed 'her', the woman he loves years and years ago.
The ending is somewhat enjoyable for me. Everyone has a happy ending that stays true (to a certain extent) to each of their personality.
The gentle Yuki lives thousands of years with Zero until he turns to dust, then gives up herself so that her beloved Kaname could once live as a human away from the complicated world of vampires and hunters, enjoying sunshine and not needing to sacrifice himself for whatever and whoever. Since Yuki is described many times as similar to her mother, I kinda expect this outcome ever since I know what her mother did for her, but I just thought the person receiving this treatment would be Zero not Kaname. I kinda thought that ! she would fiercely die with Kaname to save the two broken Kaname and Zero, heal the world and so on, so I was honestly disappointed with this ending at first. I wanted this to end with a bang and lots of tears, and with Yuki being a much stronger heroine than she is now, but I guess a moderately good ending is better for the majority.
That being said, Vampire Knight cannot be more than a 7 for me. The characters started out intriguing, but in the end none of them had the depth that I was hoping for. The plot seems grand, but feels really half-hearted and not exactly convincing. The pace remains the same the whole time, which kills off excitement and makes the story somewhat suffocating, though I do understand that the author tries to achieve a melancholic and slow tone, which mirrors the hopelessness of the immortal creatures with no ending in their battle with time, and depicts the empty hatred of the humans and whatnot. The storytelling has some bright moments; some of the monologues, dialogues, and narrative are beautifully lyrical and truly touching. And applause for the artwork.