Personally I think that up until now we rarely wait for a single episode to come out and continue playing the game from the previous one (I replayed my games once a new episode came out), so eventually we wouldn't notice the "whatness" in the previous episodes because after those come the explanation for everything, even the little details (there's a dude found some empty pokeballs in the desert, thrown by a certain trainer). I guess that we'll eventually gets our explanation in the latter episodes, and then everything would make sense.