What's stupid is to have the stories completely separated, obviously they need to follow the same storyline. What you might be thinking of is that they each go do their own thing during the same story and see different events and do different things, but not completely separated stories. Making it possible to play them separately can be good too, but they can't have nothing to do with each other, because it would tone down the importance of each, make them look like small tidbits on their own. While one big story with different sides allows for a well constructed story, especially if it's the kind of story where you have to play everyone to see the whole picture.
If I struggled to the end of my determination, to the end of my way of life with my followers, if the result is ruin, then this ruin is inevitable. Grieve. Shed tears. But you cannot regret.