Yeah, it's that weird inversion of morality that I think gets to the core of what's wrong with it. From the very beginning the World of Darkness games have revolved around playing characters who do bad things to some extent or another (greater extent in, say, Vampire, maybe lesser extent in something like Hunter or Mage), but the franchise's moral compass still basically points north. Doing bad things is doing bad things. If your Hunter or your Werewolf pack does something awful in the name of a greater good, it's still something awful. I'm sure plenty of 14-year-old edgelords played Sabbat campaigns in Vampire that just went torture-rape-murder-repeat, but the game doesn't come out and tell you from an omniscient narrator's perspective that you should feel good about your repeated acts of murder, rape, and torture.
But then you get Beast, which really does come out and say that you can do bad things and feel good about it after. And that's the bad seed all the game's problems grow out of, because if you're not a sociopath, that's not a perspective you can come around to, no matter how hard the sociopaths making the game try to talk you into it.