This would largely depend on what's the cost of given features, so it's hard to answer in vacuum.Ah yes, but what to prune?
Personally, i'd consider doing away with the map mechanics (which come with necessity to introduce tons of generic events just to have stuff happen during travels over the course of the game) and replacing it with more streamlined narrative, one that moved between key beats with occasional small events in-between. Then things like the fairies or whatever those things were in the sideplot which was effectively removed from the game during my playthrough -- this demonstrated that it'd be perfectly fine to maybe push it to a later Act without any real issue. The sheer amount of random side events you have currently is to the point where the player is going to need multiple playthroughs to experience them all. Which from the player's standpoint might be great, if multiple playthroughs are something they have keen interest in, but for developer is, as you have experienced, utterly exhausting and unsustainable. And something that could very well be distributed instead along multiple Acts.
(regarding character plot-lines, i think it's pretty easy arguments that the story main characters, that is the protagonists and antagonists, get the priority. Secondary characters are nice to have but they're secondary for a reason. There's also always a question of how much of character's arc has to be included in the game's single Act -- it can be quite okay for some to play out over longer period of time, if just to avoid the situation when it's an open-shut case in a single Act and then the writers are left scratching their heads, "okay but what do we do with these characters now")
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