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Actually, PF already has an antagonist group, three to be more exact: Team Shadow, which uses dark-type pokmon, Team Lotus, which uses psychic-types, and team Uppercut, which uses fighting-types. There's a wallpaper in the 'downloads' sections that depicts their leaders, Jewel, Lao and Brutus. Here's the link:

EVIL TEAMS

The pokmon that appear behind them are Chimplague, Ragnorilla and Despotutan, the legendaries each team wants to capture. You can face goons of the teams every now and then if you want, but first you must request Bonzai to do so. After that, a staff member will take control of the enemy using special accounts that we have created for that purpose. Direct confrontation with the team leaders is not allowed for the time being, but the possibility will be made available after a certain point in the story. Members of the evil teams controlled by us might appear randomly and without warning in the player's paths as well.

That's fine, it was a good question
The information was given in the very first post of the Trainer Sign-Up topic, so it wasn't difficult to miss it. Someday we will add a section about this to the main site.