I may have figured out a cloning exploit for Gen VI (and it may be a legacy one dating all the way back to Gen I & would work even on Gen VII too).
Instructions are as follows:
1. Trade the Pokémon you wish to clone.
2. Do not save the save with the Pokémon you are going to trash. Make sure you save the save with the Pokémon that you're gonna clone.
3. Exit the game the trash Pokémon is in, then restart. IMPORTANT! Make sure you do not save the game that has the trash Pokémon you just traded!
4. Check your party/boxes. Voila, you have a clone!
Requirements (for Gen VI/VII):
1. 2 3DSes (or a trade partner to clone with) & 2 Pokémon games that can trade to each other
2. An internet connection for the internet method (if you're doing this with someone far away)
3. Your Pokémon to clone
4. A useless Pokémon that can be trashed during this process [offtopic](cue Magikarp here lol)[/offtopic]
This is merely a theory I have. I haven't confirmed if this works or not, so can someone please test this with as many generations as possible? Also, this MIGHT need it's own topic, I wasn't sure where to put this so it's going here for the moment.