One of the differences between a normal
hexa copter and a Y6 copter is the thrust efficiency.
On a hexa copter motors are placed side by side. They do not interfere each other and deliver maximum efficiency.
On a Y6 copter the motors (props) are mounted on top of each other
(in sequence). The prop wash of the top motor/prop causes the bottom motor/prop
to perform less. This setup is less efficient. The exact efficiency loss can
only be tested in practice and depends on prop size, distance between motors, …
On a hexa copter motors are placed side by side. They do not interfere each other and deliver maximum efficiency.

On my Y6 copter I use 9x4.7 inch props. The
distance between the top prop and the bottom prop is also 9 inch. As you can
see on the graph I got a 10% efficiency loss for this setup. That is an
acceptable result.
Setup:
battery: Turnigy 3000mAh 3S 20C Lipo Pack