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I don't think you can argue that either of them is standing on terribly high moral ground as they've both done things that can be viewed as reprehensible. Lelouch killed Euphemia and Suzaku committed patricide - each for their own reasons. From the point of view of the Japanese people, you could argue that what Suzaku did in killing his father and effectively ending the fighting, fucked over the country in terms that they were /no/ longer a nation and became second class citizens. You can equally argue that Lelouch is making their lives worse by waging his war.

I don't think Suzaku brainwashed Nunnally. I think she made a choice as most of the main characters in this series has. Which is kind of one of the points of the series -- people in war time don't behave as they might in times of peace. They can and sometimes do make decisions that someone standing outside of the situation might view as horrible. And people /are/ selfish. Selfishness is part of human nature and without that to measure by, you can't really have altruism. ^^;;

I enjoy the series because there's precisely so much gray area and there's not a clear cut good guy/bad guy and that the character dynamics shift with the ongoing situation.