Sorry, could you explain a bit more what you mean when you say “they just don’t have enough phonemes for all the concepts they obviously understand”?

Let’s take an example.  Squirtle can pronounce two syllables: “squirt” and “tle.”  He can vary pitch and inflection to convey questions, exclamations, commands and so forth, but in terms of constructing indicative statements he seems to be limited to those two sounds, which means that he’s basically speaking in binary.  What’s more, 90% of what he says is just alternating those two syllables – he tends to say “squirtle squirtle” over and over rather than mixing it up the way Bulbasaur or Pikachu do (which is why I’m talking about Squirtle – when I talk about Pikachu people have an annoying tendency to worm around with the different combinations of syllables he uses, and how he has a unique utterance for Ash – pikapi – as though there could possibly be some way this had escaped my attention).  We know from Island of the Giant Pokémon that those two syllables are sufficient for him to express dissatisfaction, contentment, cynicism, humour, mockery, familiarity, uncertainty and disdain… and to comment on the weather.  If those two syllables are really all he has to work with, the range of states of mind he manages to convey over the course of that story is linguistically impossible.  Clearly there is some other component to the way he’s communicating that we aren’t capable of picking up on, but damned if I know what it is (shifts in pitch and inflection too subtle for a human ear to interpret reliably?  Body language?  Pheromones?  Some combination?).  That episode’s useful as a case study for a lot of questions because of the subtitle thing, but it’s hardly the only time we see Pokémon having conversations, and you can usually at least guess what they’re talking about (see, for instance, the scene between Bulbasaur and Pikachu in Bulbasaur’s Mysterious Garden) – they’re far from being dumb animals, and they can express their concerns to each other with, apparently, a fair degree of eloquence, in spite of possessing a minuscule lexicon.