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Well, I think that they are, in fact, one in the same.

The Raven is an agent of Drosselmeyer's Perfect Tragedy, and as such he embodies the problems the heroes are presented with and the sadistic fates Drosselmeyer has given them as their only options.

Likewise, Drosselmeyer exists as an extension of the Raven's power of people's hearts. The Raven by himself is quite the opponent. But in the end, Drosselmeyer CREATED him. All the details which lead to the Raven's sadistic final ploy were provided by Drosselmeyer. And it was only when Fakir stepped in to provide a third option that the plot could be resolved.

I'd always considered Drosselmeyer to be the 'big bad' myself, the Monster Raven taking the second place spot not too far behind; but I really do love Tesar Eshne's interpretation as well <3.

It seems like many fans still consider Rue to be a major villain of the series up until the end, despite the fact that by the finale she's more of a sympathetic character without any real power of her own (a puppet of Drosselmeyer/the Raven). I don't consider her a villain by the end of the series myself, but- other thoughts?

The Raven, Drosselmeyer was simply the writer. A story needs a villain, you can't blame the author for the villain. We don't blame Shakespeare for Tybalt.
I'm a writer myself so I understand that sometimes characters get away from the author (Trust me I killed a character without meaning to).
The Raven is the villain in this.