A villain can be as evil or awful as anyone wants to create them to be, and villain's make great main characters (Breaking Bad, Dexter, and so many other series prove that point).
My issues with villains isn't their dastardly deeds, or their evilness, but...I just find a lot of them really really boring. Villains aren't interesting to me unless I can see how their warped world view works. I want to know what makes them tick, and how they justify what they do. Evil people RARELY believe they're actually evil. Characters that are villains are still characters, and have to have motivations and reasoning behind their actions.
One of the best villains I've seen in a GOOD long time was KingPin in Netflix Daredevil. He's got a backstory that explains his reasoning for keeping power, we see why he get's so scarily angry and what motivates that, and above all else he's humanized by his love for his girlfriend. He's not a mustache twirling Rocky & Bullwinkle villain - he's got depth and form.
A good villain is one you find yourself actually ROOTING for every once in a while. A great book for breaking down villains is Bullies, Bastards and Bitches by Jessica Morrell. We used a lot of her book for inspiring and fleshing out our current storyline villain Clay "Toro" Blackthorne, Carmen Maddox & the Razors (a gang they lead) in Kamikaze.
Toro is a guy who used to be one hell of a 'good cop' kind of dude. He pulled his gang up from the bootstraps and worked his way to keep them running even after they lost crucial financial sponsorship. However, over time, his sense of justice while very much still in place, has warped to something more akin to a dictator toward his gang and his territories. He's more interested in being in power, as that's how he thinks things will stay in balance and his gang can be effective, even though the more he struggles to KEEP that power the more things will spiral out of control. He loves his city. He loves his gang, they're a family to him, and he takes acts against them personally. His reactions to slights are brutal because in his mind the only way he stays in power is by pragmatically PROVING he can keep it. And so far that's worked for him.
There's a lot more to him as a character but that's the basic gist of it. :3