I had a friend (I emphasize "HAD") who did the same thing but with Yu-Gi-Oh Cards. He kept asking to come over to play video games and duel. He always ends up sleeping over. And he had the slickest ways of cheating to get a good starting hand. Anyways, the guy took a few commons and one or two rare cards that I had duplicates of. The guy was too smart- we played with the cards all the time he was over (he doesn't have a Pokemon game- I like Pokemon more than YGO!) and my sister and I (who has no real great cards) didn't even notice that he had taken any until about a week later. We wondered why he hadn't called at all after that...
But I got them back. I never mentioned that I had been missing any cards. I prayed on his greed and told him I would give him some good cards of mine - for free. I made it very believable, and he immediately asked his parents to bring him over. When he did, me and my sister treated him like a criminal or someone who pulled a bad drug deal- I lured him into my room and my sister closed the door from the inside. We sat him down, I took his backpack (for protection and the upper hand). I told him that I knew what he did, and he denied it. We dueled for fun (that's what he thought), and I won by a mile. My sister was watching him and his hand the whole time, though she never told me what he had, just so we had proof he cheated. Eventually, I used his own selfishness and greed against him. I taunted him and totally rubbed it his face that I beat him even though he cheated and I didn't, that he got mad and stormed downstairs. He hid the cards he stole in his backpack. My sister and I searched it and found a few of the ones he took. He later admitted it and told us that he traded away the good ones. He wouldn't say what he got for them, though.
In the end, I got all of his extra cards not in his deck and the cards he stole from passive-agressive tactics. It really works, especially if the guy's greedy or selfish. You could probably use the same idea to get the Pokemon back, or another Pokemon he has of equal value. After you get him to trust you or to come over, the trick is to get leverage at first, then prey on his emotions, and finally make him admit it and/or give them back, even if you have to use the leverage you had earlier to get it. In my case, we had his backpack, with all of his extra cards and his Playstation games in it. He wouldn't trade a "friendship" and his stuff for a few cards. Sure, he did get away with some cards that he traded, in the end, I won the battle.
And I haven't seen him since. Good riddance, if you ask me!
