In this situation, Yssen fights for the Lost, the Voiceless, and for Absolute Freedom. This is of course not as simple as it seems on the surface. Most of Eorzea can go straight to the Seven Hells in a hand basket as far as he is concerned, particularly Ul'dah and Gridania. It is one of the things he struggles with. How is Gridania's zealous demand of Elemental worship not a form of oppression equal to the Empire's? How is the rich of Ul'dah's exploitation of the poor and acceptance of slavery more morally justified than what the Empire would do? He even disagrees with Limsa's current "order over freedom" policies. Decisions decisions. When you get right down to it though, if the Empire wins it will be the Lost, the Voiceless, and the Outcast that would suffer most. He just can't abide that.
"Twelve help the outcast children of the Twelve."
"Twelve help the outcast children of the Twelve."