in the second chapter of PMC, I had Hiro point out that Pokemon could understand humans but humans can't understand Pokemon. Canon-wise, this makes sense. In the anime, Pokemon seem to have absolutely no trouble understanding humans, even if they were caught just a few seconds ago. However, if you ignore anime canon, like several people on the forum seem to do, you must admit, even in the games and manga and such, a brand new Pokemon on the team seems to have absolutely no problems interpretting the meaning of an attack command they likely never heard of before. Now, there are some slight spoilers coming up, but considering they're not extremely major plot points, they probably won't make a difference. Still, avoid the next paragraph if you're wary of that kind of stuff.
I came up with an explanation for why Pokemon can understand humans like they could. Basically, whenever humans, Pokemon, anything speaks, they emmit a special set of sound waves that Pokemon are capable of hearing. These sound waves have their own complex system of meanings, much like how dolphin sonar works (dolphins do work that way, don't they?). The Nyaasu (Meowth) in the anime gets a special cameo role in PMC. After uncovering the secrets to how to pronounce the human words to these meanings, he teaches it to other Pokemon within the Rocket Gang. Because his students didn't have to discover this technique from scratch like he did, they're capable of catching on much more easily, although, they still have to deal with adjusting their vocal cords and whatnot. However, when it comes to Pokemon that can't talk.... I guess it's just basic human/Pokemon interaction. Try to guess at the meaning of body movements and whatnot, get a grip on their emotions over time, etc.