I kinda anticipated this would happen. We've been seeing more and more games sacrifice the quality of the main storyline at the expense of a bunch of side missions. I've been of the opinion that side missions that add to the story or add in a good way to understanding the game world are a good thing. However, side missions for the sake of having side missions (like we are seeing more and more often. Almost as if they are a check mark on a feature list) are a bad thing, as they usually don't contribute to the game but simply act as a way of artificially extending a game. The newer Assassin's Creed games are filled with the latter. Far Cry 3 was an example of the former. There weren't a ton of side missions, but most of them contributed to understanding the game world.
A perfect case study in a game that does open world well without artificially extending the game too much with pointless side missions is the 2002 game Mafia (I'm only going to talk about the PC version. The console version was actually quite different than the PC version. The console version removed a lot of the complexity of the PC version and instead turned it into a poor quality GTA3 clone). That game, despite being in an open world, was a linear action game. The open world was just there. There were a few small side missions that were entirely optional, though they did have benefits to the main story missions and allowed you to explore parts of the world you would otherwise likely miss. However, since there were so few side missions, those side missions were all actually quite good. They all involved stealing rare cars but in most cases they were quite different than the others. Outside of that there was only one or two small activities, like driving a taxi, that you could do. The focus was always on the main storyline and this benefited the game a great deal. Hopefully we will start seeing more games like this. It's pretty sad that this 2002 game still does a better job of many aspects of storytelling and open world than a lot of new games.
edit: holy crap someone else talked about Mafia too. At least I know I'm not that crazy then.