Here is a simple NIN setup for controller that uses the least amount of buttons and has easy access to critical functions.

First lets set up some macros:

Now go to Character Config> Hotbars> Cross> General and uncheck "Use pethotbar".

Then go to "Set Selection". Uncheck "Auto swift when weapon sheathed/unsheathed".
Then check "Enable customization when weapon is sheathed" and make sure Hotbar 1 and 3 are checked.
After, check "Enable customization when weapon is drawn" and make sure hotbar 1 and 3 are checked.
Now tapping R1 switches between hotbar 1 and 3 and skips the premade pet hotbar!

Next go to Character config> Hotbars> Cross> "Enable expanded controls" and set the (R2+L2) and (L2+R2) both to cross hotbar 2 left

Finally the actual layout, I personally use a Dualshock 4, so your mileage may vary:

Right Trigger(R2) - Cross hotbar 1 Right

Circle: Spinning Edge
Cross: Gust Slash
Square: Aeolian Edge
Triangle: Shadow Fang

Right: Dancing Edge
Down: Assassinate
Left: Armor Crush
Up: Trick Attack

Left Trigger (L2) - Cross hotbar 1 Left

Circle: Jugulate
Cross: Dream Within a Dream
Square: Mug
Triangle: Mutilate

Right: Blood for Blood
Down: Duality
Left: Internal Release
Up: Invigorate

Left + Right Triggers (L2+R2) - Cross hotbar 2 Left

Circle: Ten
Cross: Chi
Square: Jin
Triangle: Ninjustsu

Right: ShadeWalker
Down: Kassatsu
Left:Smokescreen
Up: Goad

Right Trigger (R2) - Crosshotbar 3 Right

Circle: Second Wind
Cross: Shukuchi
Square: Shade Shift
Triangle: Hide

Right: Kiss of the Wasp
Down:
Left: Kiss of the Viper
Up:

Left Tigger (L2) - Cross hotbar 3 Left

Circle:
Cross:
Square:
Triangle:

Right:
Down:
Left:
Up: