It's common to dehumanize our enemies. It makes it easier for us to root against them and knock 'em off should the need arise. As long as they aren't human, their suffering and pain doesn't bother us... in fact, it may make us hate them more.
But if you want to turn the tables on your audience so they begin to feel for the bad guy, you have make the enemy a person again. But how? The fact that they are a person isn't enough. We need to create a new kind of connection. One way to do this is spend a ton of time with the person and get to know them. This is the approach of movies as wide and varied as Beauty and the Beast and District 9.
However, if your show isn't really about the bad guys, you don't have time to develop this theme. You need a way to quickly get the audience to go from hoping the guy dies to feeling for his condition. The best way to do this: Give him something uniquely human and vulnerable to do.
In the second episode of Breaking Bad, the starved and almost dead bad guy is given a sandwich. He takes a moment to remove the crust.
He Doesn't Like the Crust
The scene could have easily been one where he gobbles down the food like an animal... and we'd further despise him. But this simple act snaps him back into humanity. He could be our neighbor, our friend, a relative, or even ... us.
Notice too: This is, in large part, visual storytelling. The actions we give our characters to do in response to situations have profound impacts on how the audience thinks about them.
Your Media Production Mentor