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I E-mailed Nintendo about whether Poke Transporter will be usable with Black/White/Black 2/White 2 after May 20th, and here's what they said:
Thank you for writing in. I can definitely understand your concerns about being able to use the Poke Transporter since the Nintendo WFC service will end on May 20th, 2014. In answer to your question, yes, you will still be able to use that service with those Pokemon games. While the Nintendo WFC won't be available, that service isn't needed since the Poke Transporter is what connects to the Internet during that process.
So no need to search high and low for that elusive pokemon and worry about time, since you still have all the time in the world (or, at least a few more years).
Dark Knight MirielxSorcerer MU Alone, they are strong. Together, they are unstoppable.