I found a video online that explained the basics of Pokemon. So Pokemon has at least 2 or 3 states stacked on each other, called a states stack. There is the Fade in state, the dialogue state, and the Play state.
Instead of this, I decided to have different rooms in the game. The player with any Pokemon left over would be their own group, by having the player carry a Pokemon bag. The opponent character with their left over Pokemon would be another group, by having the character contain the Pokemon. The two Pokemon battling would be in a Battle Room. The whole thing would be surrounded by a second Battle Room.
I'll try to make a drawing of it.
I-------I I  I I  I I  I I_______I
(I made a Football field...)