You mean like the Star Wars prequels?
We're still rooting for Anakin until halfway through
ROTS.
Carnivale is a great example of heavily featuring the villain. Generally speaking, to make a villain interesting, you've got to square him off against someone even worse. Lex was so good in the early
Smallville seasons in large part because Lionel was such a scumbag. In
Carnivale, Brother Justin also faces a bigger evil than himself... his own evil birthright.
Thing is, if the villain isn't fighting a worse villain, he becomes an anti-hero a la Macbeth, who is certainly villainous but not
the villain. Take
Downfall: for the half of the movie he's still alive, Hitler is the protagonist, holding on to hope as long as he can - a very sympathetic position. Like Lear, his madness is pitiable (I'm talking about the character in the movie here, not necessarily the historical man). He's not the Villain of the Story. It takes a hero, a la Stauffenberg in
Valkyrie, to make him a
narrative villain, in the sense that he becomes the antagonist.