I don't agree with your idea of vampire nature as inherently monstrous, especially not compared to most humans. But I'm misanthropic, and I'm also not very familiar with the World of Darkness rulebooks and official setting.
I totally agree that the game is a huge success in creating that world you describe. The cities and its characters seem so alive; I keep playing because I have this feeling that anything could happen. I love watching the story play itself out - being able to watch and act from different perspectives (clan, gender, personality) makes it that much richer.
I don't really have a complaint so much as a wish. The game seems to end with the sarcophagus exploding in Lacroix's penthouse no matter what; your main decision is whether to be there or not when it does. I wish that there were a few more possibilities - which isn't to say that the game isn't outstanding and complete as is, only that I'm greedy and just want more. I was bummed that after my Ventrue kissed Lacroix's ass the entire game (10 persuasion no less), alienated every Anarch, killed every Sabbat, we still got blown up. If you side with Lacroix, he screams 'no!' when he dies, instead of laughing like a madman when he dies by himself - that's the only difference. (And again, I found that out after playing through 3 times, *loving* it nearly all of the time, so it's not really a complaint.)
[i haven't sided with the Kuei-jin yet (or played a Tremere), so I haven't seen if that allows for other endings.]
Playing again through the early game I'm reminded of how often the Anarchs save my ass: Nines at least three times, and Jack when Lacroix throws my ignorant self out on the street in the beginning, then later when Lacroix declares open season on me towards the end. I tend to side with the Anarchs out of gratitude. Damsel lets me in to see the wounded Nines after the werewolf fight, which suggests they trust me to some extent. But that was really just to get orders to go on a suicide mission (kill all the Kuei-jin and Lacroix's people). They don't give me any warning about the sarcophagus - not even Jack, who's done so much work to set it up. I get more help from the thin blood Malkavian girl in Santa Monica ("Don't open it."), and the anonymous "Friend's" email. It hurts my feelings that, even after pledging to help and doing so much work for the Anarchs, they could just take me or leave me. *sniff*
[sorry for the post length]