I think Apple will test the waters a little longer on USB-C. It was able to be used on the new MacBook because it was basically a new product that was engineered from the ground up. The latest Mac updates didn't even add USB-C, likely because I think they just changed internals and upgraded the trackpads on these. No reconfiguration of the body required.
For the same reason I highly doubt it for the 6S. The only major hardware addition I can think of in an S-model phone is Touch ID. Everything else major -- 3G, LTE, 4-inch phone, 4.7- and 5.5-inch phone, NFC, lightning port -- has come when the model number changes. This is probably to give designers a couple of years to make major changes instead of doing it every year. I would compare it to car models going a good 5-plus years between major external overhauls. Check out the 2006 Toyota Camry vs. the 2007 Toyota Camry for what I'm talking about.
Next year I would not at all be surprised to see USB-C making its way into many Apple devices. An interesting possibility could be a USB-C/Lightning hybrid if they're close enough in specs to do such a thing. I personally would be fine with it if eventually Macs and iDevices came with nothing but USB-C ports, with the exception of maybe the SD slot and audio ports. You would think by now some standardized "one port to rule them all" would've been developed. My iMac has four USB 2, two FireWire, two audio and one ethernet port. The space taken up by the FireWire and ethernet ports is worthless to me 99.9 percent of the time. But I could easily use eight USB ports.