My reasoning is, they leave the lowest storage capacity as an entry point to people who want to get into the iOS platform. A person new to the iPhone may not want to spend the money to get the newest model, or may not think the features are worth the extra cash. They also may just not be sure if they are going to stick with iOS, so why spend the premium amount of money.
Those people who would buy the last gen iPhone, who have a little more cash to spend would then have a problem. Do they want to spend the extra money on more storage, or the newest model iPhone. Well, from Apple's point of view, they are going to want as many people experiencing the latest and greatest technology.
Plus, those people would have had 16 GB to deal with buying the last gen iPhone anyway. People new to iOS won't have a bunch of apps and photos/videos ect to bring from Android or those new to smart phones.
This is my theory at least.