Try to
hook yourself up with a beta-reader. I'm serious about this one. Your idea sounds pretty cool, but cool ideas can get slaughtered by bad execution (read: bad spelling, grammar, that sort of thing), even if you don't think it matters. (Not saying that you think that. Just saying it for the sake of covering my bases.) Your readers will have an easier time focusing on the story if you make sure your work is clean of errors (so they don't end up spending half the time trying to figure out what you're actually saying).
Betas will also help you out with characterization, plot ideas, and that sort of thing. Like I said, this is an okay plot idea, but it sounds like you haven't come up with too many plot particulars yet. Those are the kinds of things you probably won't figure out until you go and write the story. (For example, you might not figure out Character X's reason for grabbing Literal Plot Device Y until you go to write the scene. A beta-reader is someone who can help you by letting you bounce ideas off them and giving you advice as you write your story. I mean, so can the Writer's Lounge, sure, but this person is usually willing to work closer with you and will probably know your story up until that point.
Beyond that, let's talk about your plot idea itself. While a war story is interesting on the surface, there's a few things you'll want to watch out for:
1. Keep in mind the fact that Pokémon are animals in that world. Some of them are intelligent enough to rival human beings. (Alakazam, I'm looking at you.) If they wanted to build machines by now, chances are, they probably would have. Not only that, but also, even if we ignore the possibility that they're using things like that, it's still the equivalent of saying real-world bears would definitely start inventing advanced machinery if every human being on the face of our version of Earth randomly left. It could, of course, happen (which is what Mystery Dungeon sees on a level and is essentially the entire premise behind
Planet of the Apes), but it's something to think about. Why? Because I'm not saying don't have it happen. I'm saying don't have your Pokémon be people in creature costumes. Remember that they probably had to work up to that point, and remember that their technology would be different because it'd take into consideration their natural powers... and, well, body-types. (For example: dogs can't operate guns, so don't have your Growlithe do it.)
2. If you got past that tl;dr bit, keep in mind the nature of humans. Humans are pissants. They'll occupy every single part of the globe if they wanted, and they're the kind of species that aren't easily driven away. Case in point: Australia. Aside from a massive desert occupying most of the continent and an equally massive hole in the ozone layer hovering above it, Australia is home to some of its most poisonous and deadliest flora, fauna, and rocks imaginable. Yet, humankind
still decided to colonize it and thrive. If the Australians found out that an island next door is a lot less deadly, they probably wouldn't leave in a giant exodus to that other island. They'd just send a bunch of people to colonize and populate
it as well.
In short, the nature of humankind isn't to leave behind what can still be used as hospitable territory. It's to leave it
only when they'd die by standing still for five seconds with no protection. And sometimes not even then. (*motions to the research bases in
Antarctica*) Likewise for the Pokémon world because we're still talking about humans here. Humans. The species that, in that world, decided it'd be a great idea to send ten-year-olds out into the world to capture mystical beasts in baseball-sized spheres for literally fun and profit. There would have to be something major going on to chase
everyone out if they have stable establishments (read: cities, towns) there, and if that happens, chances are, it probably means the rest of the planet is rather uninhabitable, too.
Or, in even shorter terms, if you're going to have a Pokémon-only world, that's fine, but you're going to have to come up with a
very good reason why the humans aren't there but the planet isn't a smoldering boulder in space.
3. Pokémon probably wouldn't follow the same habits as mankind. As in, they probably wouldn't know what Sinnoh was, and they probably wouldn't occupy the same human cities. This just folds back into the point about not making Pokémon just humans in animal costumes. Pokémon would need time to develop. Given that humans would probably take their Pokémon wherever they went (unless, of course, you've got a good reason why they're not), we're looking at a bunch of wild Pokémon who have had little to no experience dealing with human beings. They wouldn't, therefore, have much of an understanding of human technology, and no one's going to be explaining to them what they're looking at.
Now, assuming they don't just overrun Snowpoint and destroy it (because that's what nature tends to do with things that aren't maintained by humans), this all just means that they'll developed isolated from human thought. It's like the development of a language. If you don't communicate with each other, you'll end up with different words for the same object. Likewise, Pokémon might break up Sinnoh into different territories, name it differently, group themselves into different kinds of societies (because that's also possible with human beings: civilizations don't necessarily have to live in a city a la New York), all kinds of things.
They might not even establish themselves into the same kinds of territories humans do because not all of them would necessarily behave like humans. (For example, maybe the Bidoof group themselves into nomadic tribes that travel through and don't acknowledge Shinx cities. After all, in the real world, you don't have birds acknowledging that they're living in our territory. As far as they're concerned, they've got no particular borders, so they don't really care. We, meanwhile, don't really wage war against the birds unless we're particularly bored because humans don't really think too much about it. We're different species, so it doesn't really matter to us that these animals' habitats overlap with ours.)
In other words, this is my advice:
1. Get a beta.
2. Don't think of Pokémon as human beings in animal suits. Really think about how they would develop and whatnot.
3. Come up with a
really good reason for why there's no humans.
4. Don't be afraid to think about how things work in the real world and compare it to your plot.
And voila. Fic. \o/