An under-reported detail out of E3 was Xbox head Phil Spencer mentioning that Project Scarlett would be compatible across generations. Backward compatibility is expected, an extension of the system that's already in place that stretches back to original Xbox games. But it's also going to include Xbox One controllers and accessories.
Recently, Xbox product/marketing manager James Shields reconfirmed that every Xbox One controller will work on the next-generation Xbox. It doesn't matter if it was a launch model controller, one of the newer ones with Bluetooth support, or a fancy-schmancy Elite. If it worked on Xbox One, it'll work on Project Scarlett.
Back at E3, Spencer explained that this decision is Xbox "respecting the purchases gamers have made on our platform." This makes sense as Xbox tries to blur the lines between generations, and the lines between Xbox and PC. But, it also lowers the barriers for buying Project Scarlett. Investing in the next generation is a little easier when you know you won't be gouged for the add-on accessories.