There was a lot more to the new camera than just the LED flash, so that's one thing for starters...I also wouldn't count on getting any of the features mentioned during the 5S presentation (including the burst shot or slow-mo video recording).
A7 chip comes with a slew of things that you will probably not see physically or in development for the iPhone 5...the M7 tech will mean that future movement based apps (what I feel will be a plethora of new fitness apps) will be focused solely on the 5S, but also apps based on the 64bit performance basis...this may not seem like much on the surface right now, but it's really quite impressive, and you'll see this with all kinds of stuff coming down the road, when it comes to games especially.
Fingerprint scanner is obvious, no reason to elaborate on such.
USB 4.0 for quicker transfer rates (though i don't really think this will be as impressive as it seems on paper in the real world, as most people don't really pay attention to how quickly iTunes is syncing anything on your phone)
...and you'll also be missing on improved wireless technology, including WiFi network connection improvements, as well as LTE radio antenna enhancements.