Now this is my first attempt at a pokemon fiction story, so dont criticize too harshly.Basically i was thinking of writing from the point of view of a young private in the middle of a pokemon world war,no guns just pokemon. He will end up rising thorugh the ranks over some years and so on. So i know its quite vague, but its 2 0 clock in the morning here so cut me some slack
I recommend fleshing out the story of the world war from a global/political perspective well before you start as part of your planning, even if you don't plan to focus on it (because chances are, it's going to be mentioned at least in passing, and you want consistency.) Also, the army character unfortunately has the risk of becoming a two-dimensional "Yes sir" man. If you instill some kind of brilliance but also a streak of rebellion, or a moral code that he refuses to violate, or just anything to make the character interesting, you have a good story on your hands.
My best advice would be not to follow militarism prevalent in our societies, but of what has been seen in the anime perhaps (it's good canon). However because it only shows the past, you are left with freedom in terms of the hear and now.
How much authenticity do you like? Perhaps because Pokemon is Japanese they do some things similar?