I am unsure if anyone else knows of this method, but It just came to me when I was researching for alternate ways to clone multiple Pokemon at once. Testing has been completed and this method is fail proof. It always works, but requires caution. Procedure is below.
Info:
You need to select the Pokemon you would like to clone. Depending on the time you wish to take trading, you can trade up to 936 maximum at a time, meaning you can clone 936 at one time.
A PowerSave 3DS is required. Only one person needs it over Wi-Fi. If you perfom this task on your own, you will need one.
Each person needs a 3DS console. (For Wi-Fi.)
The method may also be done using your own, 2, 3DS systems. You will also need to have 2 copies of the Pokemon X/Y game.
1. Using your PowerSave 3DS, make a backup of your save game, a backup of the cartridge you are cloning the Pokemon from. I normally name mine something like,"Pokemon Y - Cloning Backup."
2. Collect the Pokemon you need to trade and trade them to another Pokemon X/Y game on another 3DS System. (The returning Pokemon from the trade should be something of no value as it will be deleted later on. we will refer to these as the "sacrifices.")
3. Save your game. (Both consoles.)
4. On the cartridge that has the "sacrifices", load your cartridge in the PowerSave 3DS Program, and restore the previously made backup from step 1.
5. Now, you should have a backup containing the previously cloned Pokemon written to your cartridge.
6. Trade the Pokemon, Clones, from the other console back to the console in which we restored the backup.
You should now have complete legitimate clones of your Pokemon.
The method is extremely helpful tot hose who cannot complete the PokeBank method.
You can complete these steps for Wi-Fi cloning or cloning on your own 2 consoles. You must be careful with Wi-Fi cloning, make sure you can trust them.