I'm dealing with a similar problem, right now. I've had an urban fantasy kicking around in my head for over a year, and while I have a very well-developed protagonist, the villain is giving me fits.
I know what his personality is like; he's a Mafia-Don paterfamilias type who is very protective of his immediate family and the people who work for him. Enjoying his protection and generosity, however, means accepting a heavy burden of obligation. There is no question about who is in charge, and anyone who does question it gets reminded of their proper place in unambiguous terms. He's extremely charismatic, and people often feel drawn to him because he's so confident--only to discover later that they've pretty much sold their souls in the process.
He's not completely evil; he actually likes taking care of "his people." If he approves of you, he's incredibly generous and makes you feel like part of his family; you can count on him to see you through anything, if you're loyal. If he gives you his word, he will not break it. But he has an enormous need to control the world around him and force it into his ideal shape, and can be horrifyingly ruthless in doing so. Nobody defies him, or packs up and leaves, without ending up as an example for everyone else.
Oh, and he's also a wizard, from a very old magical family, and most of his followers and opponents are also witches and wizards, to one degree or another.
The trouble is, I don't know what exactly he is pursuing beyond abstract power. The usual goals of villains, such as Global Domination are just ridiculous, and don't work. "What the hell does he want? What is the goal that drives him to do the things he does?" are questions that have me tearing my hair out. I'm really no clearer on that now than I was last January, when I first "met" this character. I don't know if he's working independently, or as part of a network of similar "families" (although I think it may be the latter).
So I'm working with the protagonist and the supporting cast right now, trying to tease out their stories. The protagonist's story is very complex, and there are a lot of both major and minor characters. I may have to break this book into a series. But if there is ever going to be a book in the first place, I have to figure out my villain. Here's hoping it doesn't take 10 years...