Capturing all outposts in Far Cry 3?

If you clear the outposts, most of the enemies you face will come from missions - when you start a mission, enemies spawn at the mission location no matter how many outposts you've cleared.

Random encounters will also occur even after outposts have been cleared - for example, you may stumble onto an ongoing battle between Rakyat and Pirate forces while moving through the wilderness.

That said, most enemy forces will be eliminated if you clear all of the outposts in the game. If you prefer Rook Island to be a peaceful place, then you may want to clear these outposts. I prefer to leave the outposts alone, because I find that exploration gets boring when there's no enemies other than animals.

Currently, yes, once the outposts are cleared your encounters with enemies will become few and far between.

However patch v1.05 for the game now allows you to reset all the outposts so that you can still have enemies to face after completing the game.

Single Player: Ability to Reset Outposts

A big part of Far Cry 3’s single player experience is taking over the outposts manned by Vaas’s pirates and Hoyt’s privateers. These outposts, when taken, offer a safe place to resupply as well as a base of operations when exploring new parts of the Rook Islands.

Taking over an outpost as a player also presents a fun challenge; everything from how to approach the outpost to what weapons and tactics to use. Hence, a lot of community members have requested to be able to ‘reset’ the outposts, so that they can be taken-over again.

Here is how it works:

• After conquering all the outposts and completing the game, the player can reset the outposts by selecting “Reset Outposts” in the gameplay options menu.
• Doing this will reset and make all Outposts hostile again. All incomplete side missions and quests will become hidden. In order to finish the incomplete side missions, you will have to retake the outposts again.

Having just installed the patch myself (On Xbox 360) I can verify that this option is indeed now present.