Several well-known brands are working on this in various ways. Adidas has a cooperation with Carbon 3D to produce individualised soles for shoes you order, as one example[1]. Robotic knitting is another area I know some players are working on, for making custom uppers. You'll likely see offerings for customised footwear based on these technologies appear on the market in the next couple of years.
I'd expect it to take a number of years before the manufacturing processes have matured and evolved enough to get the price points down to the level that most people would consider an option when buying footwear, though.
I can't see cost being an issue - when you look at how shoe construction works, it should be straightforward to tweak the shoe shape for each shoe without significant increase in manufacturing cost.