Pokécharms

If by identification you mean the species, then people should be able to know the name by what they say. Although in the anime recently, an increasing amount of Pokemon don't cry out their names- likely for the sake of realism. I mean, c'mon, the REAL questions here are "Why do Pokemon cry out their names?" And "With that skill in pronunciation, why can't they say anything else despite understanding human language?"

But I digress. They probably can't identify them simply so that the show do the typical thing with them taking out the Pokédex.

That's true. You make a lot of good merit. As for your linguistics question, my answer would be that the anime humanizes Pokemon too much. Please remember that only several Pokemon are identified to having human level intelligence. This implies that Pokemon commonly have canine intelligence, where they don't truly understand human language, but can be trained to obey vocal commands.

But really, the anime was and always is lazy. They probably did that because they couldn't be bothered to recreate the actual calls, and that it makes them sound cuter. It's one of the reason I stopped watching the anime. That, and the fact they do absolutely no justice to a character's individual appearance. Aside from skin tone, hair, and eye color, they all have the same faces!