>>52306935Have them be outside of their bases and be roadblocks to the other stories if you don't deal with the main base. For one idea, they could act like trainers from other games, if they spot you, they run up to you and initiate a battle, and instead of giving you money they flee so it's a time waster. All this goes towards making getting rid of the bases an incentive outside of the Starfall Street path.
Have some of them blocking the street in Iono's gym mission so Clavell is harder to see, have them chasing away Sunflora during Brassius' mission, have a Team Star member be the one to steal the water dude's wallet and you have to find him, have a Team Star member interrupt MC Sledge, have them all constantly get in your way, and be bullies to the main character, random students, gym leader, and generally everyone, only going away once you beat the main base in that 'area'.
Maybe there could be random trainers around who you could double battle with against Team Star (randomly placed like the hidden Yiga in BOTW), and if you win the trainer you fought with gives you a semi-rare item, the point is make them more of a presence and not like a bunch of faggots who hang out in their gay labor camps.
This way Penny's reason for leaving can make more sense as they actually turned into the bullies, they were bullying instead of doing fuck all besides one cutscene at the start of the game and never doing anything of note again, and if you want to keep the same story just say the leaders don't give a fuck or don't know because they never leave the camp, otherwise have them all be dickheads who forgot what it was like to be bullied.