I checked and they weren't entirely disabled, they were just giving you the debuffs without the buffs. I fixed that and made playing the base game actually have bonuses. Mostly XP (with the drawbacks kept), but also some boosts to the other skills that can give you around +50% total bonus to those specific skills, like higher motherlode chance. I'm not entirely sure if this balances out in the correct way, so please let me know if you think something else might fit better there. The idea I had was to make the base game get the passive bonuses faster along with stronger special abilities from the other branches to compensate for not having quality.