He seems to personally dislike troublesome stuff, and only takes them on when Miyuki urges him to. I'm thinking that is an obvious sign of his own feelings and motivation.

He also likes getting the upper hand in conversations, which hints at pride, even when Miyuki is not in the room.

His choice of including Leo and Mikihiko in the team probably is due to bias. He could have worked just as well with others, but chose them.

@lelouch - He calculated that his actions are in line with the military's goals, so he was not only tolerated but even thanked for it.