Imaro
Legend
One approach to handling this - not the whole of an approach, but a start - would be for the rulebooks to talk a bit more frankly than traditionally they have about what these mechanics are for, and how they distribute authority around the table.
I actually think that the first step is for the designers to identify what the division should be in the core rules. Traditionally D&D has not been a game about distributing authority around the table, so I'm not sure if the base rules should be mixing in mechanics like these from the start. It seems more like fodder for optional modules where these type of abilities can be introduced equally to all classes and enough space can be devoted to a frank discussion about their effect on game play, how to narrate them, etc.. this seems like a much better solution than throwing a few in here or there and then having to devote the necessary space to explain the few that exist.