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You could possibly have dialogue between pokemon and pokemon since we see it all the time in the anime, and maybe the games. They seem to understand what the other is saying despite being of different species.
The downside to this, though, is that it just looks kind of ... odd to have pokemon dialect translated to English (which only the pokemon understanding, of course) and then having them revert to growls and yips with the humans. If handled well, you could probably transition smoothly between the two. Depends on how comfortable you are with the idea, and possibly how skilled you are as a writer.
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Damn, that makes all of this conversating stuff seem so risky. Though, because of the conversation in chapter three, it seems a little difficult to revert back to nods and growls and hissing. So this would be the explanation then: Pokémon talk (with him or with each other) with Keegan half-guessing/half-understanding Pokémon talk because he has learned to recognize certain pitches or certain gestures to deduce their general meaning from them (two pokémon conversating with each other makes it harder though, since he needs to adjust rapidly between languages)
Would do this do? I found both ways you pulled it off interesting and quite helpful. I'll try to keep your advice, along with all the other important stuff, in the back of my head (though visibly, I failed at avoiding repetition of adjectives, so I will really need to do my best to remember that > <)
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Random extra question: do you like 'Roy'?
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This is a question I asked, but you seem to have missed ^^; I don't demand your answer, since you seem tired and are possibly not in the mood to think about this stuff. I'd like your opinion though (if possible... Gah, repetition > <)