Back when news broke that Pokemon X & Y had been hacked, there was an immediate panic about how that would affect players. Would hacked Pokemon start circulating in trades? Would people get sucked into battles with hacked Pokemon that were impossible to beat with normal Pokemon?
While being able to generate Pokemon through external means—we're talking like, computer programs, Action Replays and such—has been happening for a while, many in the community don't necessarily feel comfortable with its existence. Arguably, being able to generate the perfect Pokemon takes the fun away from the game, and devalues the hard work of Pokemon breeders who put the time into making well-rounded Pokemon legitimately.
Purists will be purists—that's fine. But it's also possible to still enjoy Pokemon with others, even as a hacker, provided that you tell people what the deal with your Pokemon is. Transparency is key, as Kotaku reader Joseph explains in the post below this one. Then again, maybe hacking will die down given how easy it is to breed perfect Pokemon now.
It's worth noting that recently, Pokemon news website Serebii discovered that there is an easy way to tell if a Pokemon was obtained legitimately. Here's how you can tell:
In the status screen for Pokémon, and seen in trades and in the box, you may have noticed a blue pentagon next to your Pokémon. The meaning of this had yet to be determined, but has been partially revealed today. This pentagon is a confirmation of being obtained in-game. If your Pokémon has this, it confirms it was obtained legitimately in-game or through event. If not, then it has an error and has been hacked, or potentially from another region.
So unless you come across something other than that pentagon, relax: the Pokemon is legit. EDIT: The Pokemon Company defines the pentagon as a mark for Pokemon that are okay to use in tournament. It's possible that transferred Pokemon will have different marks, but we can't know until Pokemon bank.