(I bet you're getting totally annoyed with my uberlackofspaces. Okay, I'll stop now.)
My point is, creating a complex villain is just as important (and as difficult) as creating an intriguing and relatable protagonist. Your characters, like people in the real world, should not be black and white - just as your protagonist needs to have flaws, a good villain should have positive attributes to their persona while still remaining scary. Creating a nuanced villain is far more difficult than writing about an uberevilbadguy who simply wants to TAKE OVER EVERYTHING AND CONTROL THE WORLD MUAHAHAHAHAHA. (Note: Insanity doesn't count as a motive. Unless you came up with Heath Ledger as the Joker, because he was brilliant.) So I challenge you: come up with ways to make your villain a character, rather than a caricature. What does your villain want? If they are willing to kill people to achieve their goals, they better have a pretty damn good reason. What good qualities do they have to offset the bad ones?
Motivation is a huge issue with villains, and I think it's important to map out character arc and history before attempting to solidify your story. I think one of the best examples of a complex villain is Captain Barbosa from Pirates of the Caribbean. Sure, he was kind of an ass (for lack of a better term), and he's definitely the bad guy, but in the end you felt sorry that he never got to eat that apple.
When developing villains, I ask myself three questions: what do they want, why do they want it, and how do their actions oppose the protagonist?
These three questions also work for many novels in which the villain is not a specific person...for instance, The Adoration of Jenna Fox, by Mary Pearson (which happens to be one of my favorite books EVER). In this book, Jenna's main physical opposition takes the form of the government (a common theme among dystopian works - also, SPOILER ALERT).
What do they want?
The government wants to prevent widespread controversy and protest over a moral conundrum - whether or not to allow the use of bio gel, a substance that can interact with human neurons and thus rebuild damaged organs. Jenna is technically illegal (after a near-fatal car crash, her scientist father used bio gel to reconstruct roughly 90% of her body) and the government is trying to avoid the debate over artificial intelligence and whether or not a person who is 90% synthetic can actually be considered human.
Why do they want this?
Again, the government simply wants to avoid the heated political upheaval that would follow the use of bio gel to create 90% of a human brain. It is an ethically gray area, and the cultural/political repercussions could be catastrophic, particularly for the scientific community.
How do their actions oppose the protagonist?
With her reconstructed body, Jenna's existence in the US is illegal. If the government were to find out about her she could face permanent incarceration to keep her hidden from the public.
As a villain, the government has discernible, understandable goals that could have negative consequences for the protagonist.
I think we can all work on character development. It's something I've struggled with over the years, and I am constantly striving to get better, particularly when it comes to villains. Your protagonist and antagonist are, arguably, the most important characters in your story, and creating complex opposing factions gives your manuscript multiple layers and depth. I'm not saying good vs. evil stories are bad (total Harry Potter nerd here) but there's no such thing as excessive character development. For the most part, developing your villain will only make your story better.