Because your question asks about Generation VI specifically, it's what I'm going into the most detail about. Other methods for other generations will be touched upon briefly, but you'll find more information on Bulbapedia.
Generation VI
The easiest way to clone Pokemon in Generation VI is to interrupt a link trade. Please note that "easiest" doesn't mean "easy" -- the process is inconsistent and will often result in failure. It won't, however, cause any damage to your console or save file if done improperly.
You will need:
- Two 3DS systems
- Two cartridges of a Gen VI game
- The ability to perform a link trade
Once you see the blue "Communicating..." screen, start a timer. After 4.5 seconds, power off the console that traded the Pokemon you want to clone, then turn off the other one. Turn them back on to check if the cloning worked; if not, repeat until it does. This is the only method that doesn't require external hardware.
Other generations
Generations I and II share four cloning methods:
- Trading method - Refer to the Generation VI explanation above. Process will vary between generations. This is dangerous for the save file in Gen I.
- Box change method - Turning off the console as a Pokemon shifts from the box to the party
- Poke Transporter method (Virtual Console only) - Transfers Pokemon from Box 1 to the Transporter, but may leave them in the VC game as well. This often messes with the save file's music and transfer capabilities
- Storage system method - Moving a Pokemon between boxes and turning off the power while it's saving
Generation III - Emerald only:
- Battle Tower - Resetting during the save process of Link-Battle Battle Tower mode
Generation IV:
- GTS (Diamond and Pearl, impossible after WiFi shutdown) - Interrupting the deposit process to put the Pokemon both in box and GTS
- Trading - Refer to the Generation VI explanation
- Corrupted save file - Trading from a corrupted save file to get the Pokemon on both files
Generations IV and V:
- DNS abuse - Manipulating the system's DNS to connect to a non-GTS server that may provide cloning capabilities
Generation VIII - Sword and Shield only:
- Curry cloning - A party member behaving like a wild encounter after cooking Curry; able to be recaught
Generation IX
- Smeargle - Causing a wild Smeargle to use Transform and then running. This will cause it to turn into the Pokemon it Transformed into and may be caught.
- Koraidon and Miraidon - Having Ultimate Mode on the ride Pokemon and catching another Pokemon, then replacing the Koraidon/Miraidon with that Pokemon, then riding Koraidon/Miraidon again.
Cloning glitches (Bulbapedia)
Cloning Pokemon in Gen VI (GBAtemp)
I don't think I can recommend illegally modifying your products, but I can tell you that Homebrewing is incredibly simple and will allow cloning much more easily. You definitely shouldn't check out 3ds.hacks.guide if you want to learn more about this efficient process.
