Because the more pixels you capture, the more you can crop out. In other words, you get a really good digital zoom.
I shoot at 36.3 megapixels on my Nikon D800. Do I need to print something the size of my house? No, of course not. But I do appreciate getting a crystal clear photo of a portion of my photo that I later noticed would make a good shot in of itself. I use those extra pixels all the time.
That works out to a very fitting feature for an iPhone. In a rush, pull out the phone, slide to camera, shoot without composing, then zoom in after the fact and compose the object you really wanted into a close crop.
A 12MP iPhone is going to be awesome, specially with a wider aperture. More pixels produce better low light photos.