I answer this question here. However, I'll explain it.
How do I clone?
Materials Needed:
2 models of 2DS/3DS
A copy of Pokemon X/Y for each 2DS/3DS
The Pokemon you want to clone
A Pokemon you want to delete forever
(Optional) A Stopwatch for timing
Procedure/Process (Works for Patch 1.2):
Step 1: Have the Pokemon you want to clone on one 3DS, and the Pokemon you want to delete on the other 3DS
Step 2: Initiate a trade with the 3DS that has the Pokemon you want to delete
Step 3: Trade the Pokemon you want to delete with the Pokemon you want to clone
Step 4: On the 3DS that has just received the Pokemon you want to delete, wait until the "Communicating, please stand by..." screen comes up
Step 5: Put the 3DS that has just received the Pokemon you want to delete into sleep mode at about 4.5 seconds after the screen comes up. Use the stopwatch here
Step 6: Check the 3DS that has just received the Pokemon you want to clone. If it goes into a black screen that says "A communication error has occured", that means there is a chance your Pokemon was cloned.
Step 6.5: If it kicks you back into the game without going to the black screen, the clone has failed and you can try again.
Step 7: Boot up both 3DSes, and check wherever the Pokemon you wanted to clone was in the box/party was actually cloned. If two of the same Pokemon appear, success! You cloned it!
