The biggest disadvantage I can see if the lack of vendor lock in for the ecosystem. Who among us doesn't have a friend who bought the last iPhone because it "works with all my stuff' - by which they mean the 5 chargers, the custom built dock at their workstation, their car adapter, their soundsystem? Once the initial pain of transitioning to USB-C is over, the lock in is gone - here's the next gen Android phone and it uses the same port you know and love, Mr. Apple Fan Boy. The reverse is true too - people could switch from someone else to Apple more easily. I guess it depends what Apple is prioritizing - gaining market share, or avoiding losing it.
As an Android/Windows person, this makes me very happy, because in 2-3 years, people will simply ask: "Do you have a phone charger?" and literally everyone will have a USB-C cable. With the way the USB-C power spec works, it won't be unheard of to charge one phone from another - and that'll be a great way to top off a friend.