This really irks me. Without even delving into PETA as an organization, which I will refrain from doing here, they are woefully ignorant on this subject.
The thing that I find especially impressive is how untimely their attack is. Pokemon Black and White, as well as (I presume) Pokemon Black 2 and White 2, have a consistent theme regarding the well-being of Pokemon, and what it means to be a Pokemon Trainer. The Pokemon Company specifically addressed the idea that Pokemon are an oppressed, abused weapon, and debunked it with the principles of friendship, cooperation, and trust. The entire storyline of Black and White serves as a perfect rebuttal to anything PETA posts. On a fictional game. That promotes inter-species cooperation and friendship.
PETA certainly spends their time well (ok, I couldn't resist one comment about the organization, cut me some slack).