Okay, first of all this is NOT to promote my fic series. Second of all, I came up with this idea myself and do a check every month to make sure that no one has stolen this idea.
Anyway, in my fic series, all of the characters are Aquapolian. Aquapolians are half human and half Pokemon.
Calling a Pokémorph a fancy name doesn't change the fact that dozens of people have come up with the idea before you
I'm one of the old dames of Pokemorph fanfiction, and in fact, on Fanfiction.net, I seem to be known as "the" person to ask for advice on the subject, judging by the amount of mail I get concerning it. The fact I get so much mail in the first place should be a clue to the fact it is a popular genre, and hardly a new idea
But no worries - you probably didn't know
They take human form, but have one type of power, giving the Aquapolian all of the powers of the type they posess. For example, a fire type can withstand large amounts to heat and can use fire attacks.
I'm not quite getting what you're saying here. Do they have external indication of being hybrids (for example, any fur, feathers, etc) that they can hide by either literally turning into humans or through clever disguise? Or do you mean that they look totally human but just get a pokemon's superpowers and no drawbacks? The latter is dangerous, thorny Sue-territory. While it's possible for a character with multifarious unnatural powers to be well rounded and unique, it's usually just begging for trouble, especially in the pokemorph genre, which is a giant minefield of cliches. Basically, hybridizaton should almost never be "perfect" - getting only positive benefits and nothing of the negative. Instead, there should be a balence - they might look perfectly human and have pokemon superpowers, but suffer a somewhat animalized mindset due to their pokemon genes, for example.
Now, there is a back story to this race. They formed 16,000 years ago
How? Hybridization can occur in nature, but what on earth would have possessed a large enough group of people (especially since you said you're using the Poke-earth is our earth theory of canon, and bestiality is a very ancient taboo among virtually all human cultures) that having sex with pokemon was not only okay, but that the fact they were producing freakish offspring (since obviously genetic engineering would not have been around in BCE) was fine and dandy, too?
and were nearly destroyed by a Great War between Kyogre and Groudon 3,000 years ago.
How and why? Why did Kyogre and Groudon not like the pokemorphs?
True, there are humans in the world (which is our world), but they are being threatened by a force that is trying to kill them. The Aquapolian nation is peaceful, but only two people know their language which was lost during the Great War: The main character and her mentor.
This doesn't make any sense. Obviously, these hybrids must have been breeding with a heck of a lot of humans to get all trace of an outwards pokemonlike appearence from their genes (if that's in fact what you meant). What happened in the war that made them isolated, no longer seeking humans but only, apparently, breeding with their own race? And the language would not have been "lost" if there are active speakers. A language is officially classed as dead when there are no living persons who can speak it. Obviously, some humans must have known the language to be able to pass it along to the main character and the mentor. That would, of course, render it as not being lost at all (and if Aquapolians [and I agree with others that this really does need a different, less watersounding name] are supposedly dwelling in our modern world in a collective nation, shouldn't their culture be well known and documented? We
do have helicopters, TV satellites, etc. Also, if they're such pacifists, why would they not willingly speak out to humans in wartime? Where are they living, besides a weird mix of Switzerland and Tibet?
Anyway, tell me what you think of the concept of Aquapolians and do I need to fix something in it?
A lot of things still need to be thought through - however, I do like to say no idea is hopeless, so don't give up