Hi Trihan, I actually implemented a passive skill system that requires minimal plugin (mostly just YEP Skill Core), as the notetags there are just to add stats or for other checks (e.g., if the character meets the skill requirements), while other effects rely on other notetags.
Example, I have a weapon specialization passive skill that adds a 50% damage increase to the weapon, but instead of a notetag in the skill, I used Ramza's weapon damage formula plugin and have the notetag in the weapons instead. Hence, there should not be too much of a compatibility issue, I think?
The passive skills I am thinking of causing class name changes are actually related to the class system I implemented, as rather than actually changing the class, I have classes that are tiered, and each "base" class can advance in a few different directions (e.g., a mage can advance to a more support/utility based class or a DPS by "learning" the "advanced" class). The plugins that would affect the passive skills are YEP Skill Core, Skill Learn System, perhaps Skill Mastery Levels (more to set the skill max level as 0 for passives).