Well, actually, this isn't a cheat. But it is about cloning Pokemon!
You CAN clone Groudon, Kyogre, and Rayquaza! It's true!
One of my friends cloned some of her Pokemon (Groudon and Rayquaza), and it worked!
I battled her with some of my Pokemon. She had two Groudons and two Rayquazas.
No, she didn't catch one of each and got the other two from a trade.
She cloned them! I know this because the Pokemon ID numbers were the same. (That and the OTs were the same as well.)
Like I said, you can clone those three pokemon! Thank you for your time, try the cheat!