I thought that the most plausible explanation for why Apple ships a 16GB base configuration is this: There simply isn't enough supply of NAND in the world to add a 32GB chip to every single iPhone in the world.
If that were true, though, I am not sure they'd still be doing it again this year. I think that it's a business decision spurred by the knowledge that far more people will be willing to spend that $100 extra to jump from 16GB to 64GB. Still, if Apple values the user experience of their products above all else, that seems like a short-sighted move. Let's hope this gets improved upon when the iPhone 7 (or whatever it's called) launches.
Considering they will have sold 240M Iphone 6,6+ (almost 50% more than the 5s), I think Apple knows what their client really want (more than so called "experts" here).