Far Cry 3 does a lot of things right. It's fun to play, the island setting is beautiful, sneaking around is a lot of fun, gunplay is solid, and everything works well. But the story… well, the story has some issues.
As I pointed out in my review, the unevenness and general kinda dumbness of the narrative is the thing that holds Far Cry 3 back from "we'll still talk about this in five years" glory. I'm midway through my second playthrough, and the problems with the story are more apparent than ever.