This special 3DS XL will not come bundled with a copy of Yoshi's New Island. The game will be sold separately to the themed piece of hardware. If you get the game, it will run you an additional $39.99 (USD) on top of the price of the console.
Though you'd have to pay extra for Yoshi's New Island, you can still get a free copy of Pokemon X/Y if you register both your new 3DS XL and Yoshi's New Island at Club Nintendo. Simply do this by March 31 to get your free copy of Pokemon X or Pokemon Y from them.