One of my biggest problems with Far Cry 3 is the complete disappearance of enemies in areas where I've cleared outposts. I really like the sense of constant danger their presence provides. It seems that others feel the same way, as Ubisoft is implementing a patch that will allow us to reset every last one of them, a feature apparently requested heavily by players.
In an Ubisoft forums post, they've also announced the new Master difficulty, which makes things even scarier in the jungle. I like that. There's also changes to the way sharing player-created multiplayer maps works, with a new feedback system, spectator options, and the ability to find maps by author. You can now skip maps and don't have to worry about being booted from custom game types either, which is nice.
Read all about the changes over at the Ubisoft forums.