Feel awful? Well, not really. I’m not sure if you’ve read it, but I have dealt with the subject in some depth in the past – it’s probably the most popular thing I’ve ever written. Basically it all comes down to how much choice you think the Pokémon have in the matter, and I tend to think the answer is actually “quite a bit.” http://pokemaniacal.tumblr.com/post/34093585438/the-ethics-of-pokemon-training
The article you mention – here’s a link, by the way, for other readers http://ladygeekgirl.wordpress.com/2013/08/31/in-brightest-dayish-the-pokemon-problem/ – well… I mean, yes, obviously, the complaints are fair, and I think it’s best if we keep those in mind. I also think the franchise produces by far its most interesting stories when the developers keep them in mind, and the same goes for fan fiction. It’s not exactly a clever point, though. I mean… I don’t think people should get to say “Pokémon portrays violence involving animals” as though it’s a great insight. Don’t just say it; work with it!
EDIT: Oh, yeah, you asked about X and Y. Well, I’m not all that far in yet, so I don’t really know. Still haven’t found out what Team Flare is really all about, or what Lysandre has to do with anything (I mean, I assume he’s important, and the game keeps dropping hints that he’s a bad guy and maybe the leader of Team Flare, but his ethos doesn’t really seem compatible with theirs, so eh?). I’ll keep everyone posted, of course!
DOUBLE EDIT: People really say “yo yo yo”?