Any ideas what sticks around once you finish the game?

We work our way through each area, essentially "liberating" it and then we kill the main baddie. What happens then? It seems like once we have "liberated" a zone there are a lot of rebels, and not a lot of enemies. So in the end will the map just be covered with friendlies?

Any PvE to be had once the main story is completed? Aside from the repeatable "side quests" which don't provide much challenge.