Watched The Prestige with someone who hadn't seen it before the other day and realised that on first viewing Angier is the hero up to the point when he sends Olivia to Borden. Up till then he's by far the more attactive character, and Borden is the villain who seems to be responsible for killing Angier's wife.
This changes completely after he sends Olivia to Borden and we see that he has been overwhelmed by obsession.
Both characters are pretty villainous, albeit in their own ways. I'd hate to say that one is "more of a bad guy" than the other. A lot separates them but it's their ultimate obsession with petty illusions that really destroys them.
Location: We can't stop here, this is Bat Country!
All Nolan films go beyond the simple perception of good and evil, most of the times the characters follow their own perception of such extremes meaning the director - may believe whatever we construct within our minds is as valid as whatever is in the so called: real world or outside world.