I've really enjoyed Vampire Knight, even with the sappiness and kind of random plot twists, that's part of what makes it fun - after all, it is supposed to be entertainment.
I can honestly say that I feel for all of the characters (except maybe Rido - guy was a total douchebag), but that definitely doesn't mean that I agree with everything they've done.
People will probably (no, definitely) flame me for saying this, but having been a confused 17 year old suddenly dumped into a situation that I wasn't prepared for, I can't bring myself to hate Yuuki. Yes, I would really like her to be more assertive about her decisions and commit to them wholeheartedly, but at the same time I can understand how that wouldn't be easy.
Yuuki & Zero (talk about Kaname in a second) - they're both teenagers and they've both hurt each other trying to deal with their own crap while still trying to watch out for the other; Zero points guns at her head and threatens to kill her every other chapter but won't actually do it because of his feelings for her; the more aggressive/hurt he acts, Yuuki protects/loves him more and then gets confused because of her feelings for Kaname and so the cycle goes.
While I think the memory rape thing was an arrogant and selfish action on her part (when someone says stop, you probably should), I agree that she felt it would be in Zero's best interest and since I wish some of my exes had done that for me - can't hate her for it. The fact that she gets pissed off and slaps Kaname for acting like a turd shows that she is sticking to her reasons for erasing Zero's memories in the first place - she doesn't want him to be "dragged into [our] lives" and that near to her "isn't a place [he] should be" because he seems to get hurt or endangered somehow every time they are around one another (strengthened by the fact that Kaido and him come under attack on the final page).
While I think I understand Zero and Yuuki's objectives and motivations, Kaname, not so much. I'm drawn to him because I'm a sucker for bad boys, so can relate to the attraction/connection Yuuki feels for him, but as a reader I don't get what drives him as a character.
The easy answer is "He's done everything to protect Yuuki, and will keep protecting her in any way he thinks best," and that comes from how he loves her, but that explanation seems flimsy at times. I guess what puzzles me most is the lightning fast changes in his declared tactics - first we'll kill the council so she won't have to worry about nobles, then that isn't good enough so we'll kill the other purebloods, nope that's still not good enough so I'll throw myself into the furnace to become the 'parent'. What is the trigger that causes the change in tactics? If his ultimate goal was to become the parent in the first place, then why tell her that he loves her and they will be together for eternity if he's already planning on jumping into the fire?
Perhaps Hino Matsuri is trying to demonstrate what happens when people love someone but don't know how to love?
He obviously loved the ancestress (who's a lot like Yuuki - she wants to protect humans, and would rather sacrifice herself than the person she loves, except the ancestress wasn't 17 ), but couldn't save her from her own sense of duty/doing what was right, so when he gets a second chance at love with Yuuki, instead of loving he's too busy protecting (regardless of the cost to those around him).
While I am not a shipper, I'd recommend listening to the song "Gravity" by Sara Bareilles as I think it really neatly sums up the Yuuki x Kaname relationship.
Basically, I think all of these characters are beautifully flawed and I find the series very moving even if it aggravates or frustrates me.
If you've stuck with me this far, I thank and commend you :)