If programming is a way of thinking/problem solving, I'm not sure how supplying the context in line teaches you how to think -- as opposed to sitting down and figuring out a problem on your own.
My experience has been that the best way to learn to program is to try something out for yourself. Whether you write it from scratch or use example code to help you get started. It takes a bit of time, but you get better at it.
You need to be able to sit down and spend the time thinking to solve a problem. It's actually quite hard to teach this even in school -- I honestly believe that the main advantage to taking a CS degree over using the internet to learn is that you are actually are forced to group together and work on projects whereas a self study course would not enforce that.
Often the best way to make something more mainstream is to "dumb it down". I don't think it's because most people aren't intelligent enough, it's because it needs to have mass appeal, and therefore needs to interest a wide range of people. Doing this with programming is quite hard if programming is a way of thinking -- how can you "dumb down" a way of thinking to make it more appealing when a lot of programming is dealing with detail.
The thing about flow, if/for statements, is that you tend to master them very quickly. While the visualizations are cool, they have very little usage beyond the first 3 or 4 lessons.
Very interesting examples, but I don't see these examples helping out much more than other sites (I agree that sites that CodeAcademy aren't at all how the press/Mayor Bloomberg/TechCrunch makes them out to be).