One step to an effective arc is not just to get your character up in a tree and throw rocks at them; it's also to figure out just how that tree/rock scenario affects your character.
Pain changes your character. It's important you know how that character handles it.
Weird question, isn't it? But if you don't know the answer, your characters might not be 3D.
Your characters didn't appear the moment you write the first page. Just like in your own life, they were influenced by someone else—for good or ill. Understanding why your characters respond the way they do is crucial to character development, and knowing who influenced them is a key part of that.
Why does this matter? Because if you're not writing your villains with the awareness that in their head, they're not the villain, you may be writing a flat, 2D character.