Until now, Apple has never intentionally made a less capable phone. Every model (aside from storage capacity) has been the most capable phone they could make at the time it was designed.
Since the 3GS, Apple has always offered the previous flagship model at a discount. Nothing about the previous model was changed and certainly no capability was removed. The previous model didn't have the capabilities of the current flagship model simply because the capabilities were not available when the previous model was designed.
I think this new direction apple is taking will be more obvious when the next 2 models of iPhone are released. Right now, the iPhone 5c is just as capable as the iPhone 5. The only difference is the exterior. I think when the next models of iPhone are released, you will find that some capabilities of the current iPhone 5s will not be passed on to the next non-flagship phone. For example, perhaps Touch ID will only be available on whatever flagship phone is selling at the time. Meaning the only way to have Touch ID is to buy the current flagship phone, since the previous flagship phone will no longer be available.
I'm not sure what the cost difference is for Apple on the iPhone 5 vs the iPhone 5c. I understand that plastic is probably cheaper, but you have to also consider the additional cost of redesign and additional manufacturing. The iPhone 5 is a turnkey product. It's cost of design and new manufacturing has already been filled.
I think the biggest cost advantage for Apple will be in future phones. I think this is simply laying the ground work. You will never again be able to buy last years model. And the current cheaper phone may end up being less capable then the previous flagship phone.
This is where it gets confusing.
Next September do they offer the 5 in place of the 4S, or is it the 5C? What then replaces the 5C? Does the 5S get dumped entirely?