right, so the main plot of season one is going to establish the world we live in. The relationships between kingdoms, the characters, the relationships the humans have with the pokemon. By the end of the first season, the story begins to pick up pace and things get serious.
Season two, the Dragon King begins his march across across the country, trying to take over the surrounding lands. The Rebels begin their assault from within. Matt returns home and joins his father's army. His father is getting ill and his mother begins to have an affair with his uncle. Isabel begins peace negotiations with the Dragon King, but when that fails she provides support to the Fire Kingdom.
During both seasons there will be filler Episodes about the Psychic King and his adventures, but his real involvement in the plot won't come until the end of season 2, where they defeat the Dragon King and Zoroark has transfered much of the Dragon Kingdom to his own Dark Kingdom.
Season 3 will have the Water Kingdom become swarmed with far too many Pokemon, causing them to seek the aid of the Fire Kingdom, but the resulting chaos leeds to the destruction of the capital. Isabel and her Husband sign a deal with Matt's uncle who has now become the king, taking the place of Matt's father who is now dead. Unfortunately, the Fire Kingdom itself has not been able to stop the increasing swarm of Pokemon, causing the Fire, Ice and the Grass Kingdom to fall. The four kingdoms are forced to form an alliance to try and stop the constant swarms of Pokemon.
The Psychic King has begun to learn of Zoroark's plan due to accidentally teleporting to the room where Zoroark fought the Dragon King for power. After he ends up teleporting to the camp of the four kings, he explains what has actually happened, but first they have to deal with his own Pokemon problems. After the alliance of Pokemon and humans have formed to combat Zoroark, they go on to war again.
After Zoroark looses, he gets captured by the Industry and they force him into servitude and season 4 comes about. The Regalex, the new name of the Alliance, including the Psychic King, who has taken province over the remains of the Dark Kingdom since ther monarch was a pokemon, and the Dragon King, the once former leader of the Dragon Rebellion from season 1 and 2, and the previous four kingdoms of before.
but sadly the alliance is in trouble because the constant wars have dwindled their collective economy. the dragon kingdom is the only remotely stable economically, but not enough to support the other five. So the Industry steps up, offering financial stability to them. They welcome the aid until the current Dragon king brings a secret meeting involving the kings only, telling them of the notes he found in the last Dragon King's study. He tells them of the Industry's danger and warns them about accepting too much help from them.
I'm a little lost on how the events of Season 4, since I don't want a third war. We've already had a Human war and Human vs Pokemon war. I want this to be something different. Maybe we could let the real threat of the Industry stay silent still for another season and bring the season to a more personal level. use this one to go back to season 1 with more focus on character development. and we could go into a Hamlet plot with Matt and his uncle