It's kind of funny that in open-world games, especially ones of the fantasy variety, story is put on the back burner and exploration and going all stabby/ blowy-uppy gets the limelight. That's not to say that more linear story-driven games are superior, as my often relied upon example of Dragon Age 2 proved, despite my praise of the writing. However, in the final year of this incredibly long and epic gaming generation, it seems that story has been brought back to the forefront, at least thus far. It is only February after all.
Maybe it's that story mechanics make it easier for the developers to show off what they can do with relatively ancient tech. Games like DMC and Ni no Kuni show off particular styles and level designs while arguably providing some of the strongest story telling, among AAA titles, in the last few years. Both games also play very smoothly and look fantastic. As a side note, these are what consoles need to continue supplying in order to to survive: strong original story telling, pretty graphics and great game play.
Upcoming games such as Crysis 3 and Bioshock Infinite have the potential to continue pushing FPS' as not only ways to show off how good you are at head-shots, but as great means of telling great interactive stories. With the right creative teams and enough visual style (much like Far Cry 3's realistic, yet unique style) to make the games unique, these games could really help push game design, even high-budget titles, as a real art-form.
There are examples where open-world elements are put into story drive games. The Witcher 2 and Dishonored come to mind. The issue is these aren't neccesary open-world games. Far Cry 3 seems to have an intriguing story and hit most of the elements on the head, which could make it the prime example of what I'd want out of an open-world game.
I'm hoping developers continue to push the envelope on what to expect from open-world games and games in general. I want to have the shared experience of exploring the world with a great sense of purpose and to uncover a fantastic tale. For the most part, the two feel like either-or situations. It could very well be the limitations of consoles, or it could be a creative decision. Sounding like a broken record: I'm much more interested in a great narrative than having a seemingly random excuse to go and explore a world. Why can't the two be one?