Fastest way to migrate data from Late 2016 13" MacBook Pro to 2009 Mac Pro
You have three options to connect two Mac's together to transfer settings via Migration Assistant:


Ethernet
Firewire
Thunderbolt


There's no option to connect via USB.  Academically speaking, connecting via USB would be your slowest connection because it's only 480Mb/s (USB 2.0) versus Ethernet at 1Gb/s or Firewire 800 at 800Mb/s.  Thunderbolt isn't available on a 2009 Mac Pro

The easiest thing to do is to get a USBC to Ethernet Adapter and connect via the onboard Ethernet on the Mac Pro.  I recommend this over the Firewire for three reasons:


It's faster than Firewire
You probably already own a Ethernet cable; you would have to purchase a Firewire cable specifically for this
You are more likely to need the Ethernet adapter than you will a Thunderbolt to Firewire adapter