What is cloning?
Cloning is the exploitation of bugs/glitches in the game to "clone" a Pokemon, or make an exact replica of the Pokemon that is cloned. Same EVs, IVs, Level, PVs, Item, PokeRus, everything! This is normally used to clone legendary Pokemon or 6 IV Pokemon to trade without losing the original Pokemon.
I would never recommend to clone.
How do I clone?
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!
You wait 4.5 seconds to clone due to the fact the game calculates when each Pokemon goes on the other system separately. For example:
0 Seconds --- Trade Complete
0.5 Seconds --- Initiating transfer of [Pokemon 1]
4.5 Seconds --- Transfer of [Pokemon 1] complete.
5 Seconds --- Initiating transfer of [Pokemon 2]
9.5 Seconds --- Transfer of [Pokemon 2] complete.
10 Seconds --- Transfer complete, goes back to trading screen
As soon as Pokemon 1 (the cloned Pokemon) is transferred, it is actually on both 3DSes. If the power is shut off at this time, Pokemon 2 (the deleted Pokemon) is stuck in transfer while the cloned Pokemon is on both 3DSes, therefore deleting Pokemon 2.
Explained in this video