Just watched all 12 episodes over the last four days. Outstanding series. I wanted more closure out of the finale, but upon reflection, I really appreciate how it played out. It was just so very well done and well acted.
On his motivation (re: love for Issa vs. his own kids), Brody was doing it for his kids. He felt that was extreme injustice in the world, and the leader of that injustice was soon to be running the country his family lives in. In his own jaded sense of purpose, he thought that he was doing right by his family.