A Pokemon war? Sounds interesting. Usually within a story, there is a theme, or a deeper concept. The armies will usually represent different views of the argument; and the focus usually isn't on the battle itself, but typically on the leaders who we know more about. (or maybe the POV is one of the grunts)
I think that the build up to the battle is just as important as the battle itself. While this may seem obvious, consider the following:
Why is the battle happening?
What does each side have at stake?
What is an absolutely unacceptable loss for each side?
How does each sides people feel about the war?
What is the setting of the battle? Why does the battle happen at the selected location?
Historically, battles would often happen in
Open fields (Enables the greatest use of traditional flanking tactics)
Hills (For when side is attacking another, the hills provide a terrific defensive advantage. Also, ambushes)
Forests (Especially in closer to Modern times, given the number of forests the U.S. was in during war. forests provide natural cover against ranged attacks)
Additionally, realize that each Army will likely be divided into different groups, or divisions, based on their function.
Infantry (Ground based pokemon) The main ground unit of an army.
Artillery (Long ranged Pokemon. Anything from small attacks (kinda like bow and arrow in real life) to large attacks (like cannon balls). Artillery timing is fairly complicated;
whether they are firing at will (as soon as they can) or in barrages (everyone shoots at the same moment). Well timed barrages can be devasting, either softening up the opposing army line, or shattering an enemy attack.
Flying Divisions/Particularly fast pokemon - In real life would be cavalry, or air assets - These are great at running disruptions; hitting the enemy where they are weak.
In battles, flanking an enemy, and also having the high ground are two of the biggest factors to strategically winning a battle. When Flanked, an enemy is attacked on more than one side, which leads to chaos. It's very hard to defend against enemies from two directions. Additionally, when an enemy has to go up high ground, they will be tired; which is a serious disadvantage.
Since we have pokemon though, we can get far more creative.
Water pokemon could turn the ground into mud; Pokemon stuck in mud would be slow; perfect for artillery units to destroy.
Fire Pokemon could light the area on fire; burning the enemy out, creating large smokescreens (which way is the wind blowing?) that not only obscure a target, but if thick
enough would cause them to choke; which would be really disruptive.
Flying pokemon can drop in batches of ground units, kind of like paratroopers dropping.
Additionally, given how significant type advantage is in battle, divisions would also have to strongly consider type advantage. Artillery may have electric types, especially to deal with an enemy flying division.
A heavy fog could help an army sneak up on the enemy without being noticed. If your army is obscured by woods, fog, smoke, nighttime, heavy rain, etc, then enemy artillery will have a hard time effectively shooting at them. So if I had mostly infantry, I would try to sneak attack an army with tons of artillery a) when they least expect it b) during horrible weather, and preferably at night so they would have the least chance of hitting.
And on and on and on.
Just don't forget! There is typically a larger conflict in terms of the theme that is stake in the story, and you can't forget about it! If you lose sight, you may have an awesome battle, but the story could suffer for it.
Happy writing!