The story missions is where most of the fun was in Far Cry 3. In Far Cry 3 I'd just teleport to a nearby liberated outpost, drive 2 minutes and start the mission.
So what if everyone in the world magically knows I'm the enemy? We've experienced this sort of thing for as long as videogames have been around. I equate immersion with how well the game keeps my attention no matter what it does. I don't equate immersion with realism in the least. In that way, the game feels much more immersive than Far Cry 3.
The more enemies the better, so it feels like a real struggle to get from point A to B, and there are a lot more opportunities for fun things to happen. I actually like how practically everyone tries to kill you in Far Cry 2, and I couldn't care less if it makes any 'real' sense.