Recently, many players (including myself) have been disappointed with the post-game character model of Connor, being that his hood stays down. Now, I myself have found a remedy to put his hood back up. What you need to do is go into the Aquila missions, and choose Dead Man's Chest. Note: you need to have not completed it when you do this. It cannot be a replay of the mission, it has to be the first playthrough of it. Also, doing any other Aquila mission WILL cause his hood to be placed back down.