Not all stories need villains. Not all antagonists need to be bad. And, when you can give the bad guys good points, that adds dimensions to your story.
There are lots of ways to create and enhance your villains, and I wrote about some of them in a five-part series that began last March. Today, to continue Try This at Home, I'll introduce three things you can experiment with to make your villains more difficult to handle because none of them hit your heroes in straightforward ways.
He's so nice. One way we deal with real-life troublemakers is by sharing thoughts and experiences with other victims. Even if these don't prepare us for the next assault, they validate what we went through and make us feel less singled out and alone.
Which is why making the villain seem nice to others is so painful for your hero. No one believes he acted so viciously. They wonder if your protagonist is paranoid or cruel. How can he or she say such awful things? Whenever your protagonist is isolated, the burden of abuse becomes harsher. If you make everyone around your hero a fan of the opposition (or at least sympathetic to the bad guy -- seeing him as the victim), every complaint gets stifled. Every action aimed at escaping persecution is questioned.
Put this into action by seeing if your villain can, minimally, make someone dear to the protagonist into a loyal ally.
You're a bully. When the villain is seen as wronged, weaker, or downtrodden, he gets a strange power. People root for the underdog. They want to champion the oppressed. I remember Danny Simon saying that Michael J. Fox's character in Family Ties could get away with anything because he was so small. Standing up to him would automatically make you appear evil. But imagine being at his mercy instead of safely in the audience?
I remember, back in the days before credit cards were ubiquitous, a baseball hero of mine took his savings and bought a sports equipment store. One by one, the local Little League teams outfitted themselves on credit and didn't pay their bills. They bankrupted him and forced him back out on the road as a radio announcer. They were villains who knew his complaints would make him look like a bully.
See if you can find a way to give your bad guy the appearance of being powerless compared to our protagonist.
Winning is the only thing. There are villains who are so obsessed, they have no limits. They'll damage themselves rather than lose. Certainly, mobsters who are so ruthless they kill off whole families create shock and can terrorize their victims. But there is a special fear when the bad guy seems to have slipped off the rails because he is willing to see those he himself loves get hurt rather than suffer an insult.
An example of this in real life that might fit this, depending upon your point of view, is Gordon Liddy holding his hand over a flame to make a point. If you take your villains and mess with Maslow's pyramid of needs, giving them priorities that lead to their accepting horrible losses and the unimaginable will become all too real.
So put your hero up against someone who vividly illustrates his "natural" responses are inverted.
Note that none of these explicitly target the hero or, by themselves, cause him harm. You can disadvantage your protagonist (and shift the balance to the antagonist) in many ways that are indirect. Passive-aggressive actions, gaslighting, and enticements that reveal the flaws of the main character all fit this model. And they are all difficult to defend against.