I really wish that games like this would do a better job of incorporating the side missions into the story. There needs to be more of an incentive to do them. In this game, I attempted to do side missions in the beginning, but I soon realized that they weren't helping me accomplish anything, so I stopped and just focused on the story. Much like the last game with the weird roof attacks, once you do the initial tutorial mission, you never have to do anything like that the rest of the game. Once you finish the story, you just end up back in the world with all this random crap to do.
Well, i thought the homestead missions where a nice diversion and they helped you get better gear...