This is set to change in iOS 8 - Apple has dropped a few hints about its plans at WWDC, and it seems like the company will give users access to just about every single manual camera setting you can think of in the stock app: ISO, shutter speed, focus, white balance and exposure.
What does this enable? Controlling ISO manually, for instance, allows you to control the light gain (or light sensitivity) of the sensor: setting ISO high translates into more light passing onto it and brighter images, but it also entails more noise. The shutter speed, on the other hand, refers to the time the sensor has to absorb light, and the longer it is, the more light it can absorb.
We don’t know whether Apple will open up access to those features to third-party apps as well, but if it does, we might just see a flood of new iOS camera apps. What seems certain, though, is that Apple is taking the camera parts of the iPhone seriously, and we're about to see plenty of progress in iOS photography in the near future.