As an imperfect way of causing the human player to consider the risks and rewards of a high degree of powermongering and of spreading out aggression over time it works great.
And imperfect is as good as it gets in any solution.
In other words, while there's plenty to say about the BB concept from a "does this make any sense at all, historically?" and most of it bad, it remains a pretty good game mechanic so long as it is completely transparent to the player what is going on and the later games have been great in that regard showing you exactly how close you are to going over your limit and gradually making things harder for you as you accumulate badboy points without it becoming punishingly hard.
Having things like badboy wars kick in at the last stage is again a thing that can either challenge a player (because such wars are winnable) or act as a cautionary foil (because he would rather not end up in such a war) depending on his interests in and motivations for playing.
It may be that active spheres of influence will tune down the need for a badboy system while players are pursuing very limited goals, but I doubt it will eliminate the usefulness of having a badboy system or equivalent running as the final check on great ambitions and providing players with a challenge*.
and this is important when making a game rather than a simulator, even if not all players play to be challenged.
