I don't like the idea of cloning shinies to trade for stuff. I'm a firm believer that you must lose something to get something in return; by trading clones you completely bypass the part where you lose something.
The Law of Equivalent Exchange might say that, but I personally disagree.
This discussion reminds me of duped items in online games.
In the case of Pokémon, it does defeat the point of trading and uniqueness, but at the same time, I absolutely hate the idea of how some Pokémon are only given out at specific events. It's not that they're hard to find in-game, they're just completely impossible to get without events that aren't available to everyone. Cloning makes legit events much more accessible to people, so I appreciate that it's there. If there were no events or one-shot Pokémon though, I would probably disagree with it.
At least you can't really make money off cloning Pokémon, as is the case with duped items online (oh dear, the item shops...) because cloning is much more accessible.
BTW, ares is right in that there's no original or clone. IIRC, the GTS cloning is done because of save corruption during Wi-Fi communication. There's no "original" in that case, it's just that one comes from an older save. So you never have the satisfaction of thinking "well I have the REAL one!" or such. I think this applies to duplication in other games, too, but correct me if I'm wrong.