If someone posed the question "should I use my only upgrade, or pay money to buy outright, the 5S if I am coming from an iphone 5" I would say no. I would say hold onto that upgrade, or save that money, and continue enjoying the iphone 5.
But if someone is asking, "should I use my upgrade or new line to buy the 5, or the 5S, as I am not a current owner of either" I would say get the 5S. Particularly if a) the money is there and b) you plan on holding onto the phone for 2 years. The A7 processor will likely be a key when you go to load IOS 8 and IOS9 onto the device. You will be getting slightly, and I mean slightly, better battery life. Slightly better camera. M7 processor. 64bit chip which may come into play down the road. All around, it is a better phone. Plus, you may see better resale value at the end of the two years for the 5S vs. the 5.
Good luck and either way, enjoy the phone you decide on.