On antagonists who just want to be understood

I was reading a graphic novel, and I had an epiphany about why the Napkin Epic is stalled: I am trying too hard to make the antagonist not a completely bad guy.  I am making too many excuses for his (completely rational but somewhat harsh) behavior.  I want him to be understood, to not be a villain.  I am killing my story where it stands because I want people to know the antagonist's motives and his suffering and all that good stuff.

Thing is, with the narrative structured the way it is, that really can't happen, and the answer is not to restructure the story but to let him stay more in the background where he won't be talked about and explained to death.  He needs to be a bit mysterious and unknowable.  It's okay, yea, necessary for him to be so.  This means that people won't necessarily understand him and know everything about him that I do, and this is really okay.

Since he will never be physically present until near the end, his dialogue can't do much to reveal his character, and having other people give speeches about him is also not the answer.  I will have to work harder to reveal his character in bits and pieces the reader can pick up from other people and from his actions as they affect the characters in the story.

Drat.  It's way easier to just talk him to death.