This is definitely something that I've been thinking about. The intention when I first started, was to have a bunch of branching paths, both big and small. The Brutus one absolutely turned out way bigger than I expected. So after I finish this one, I'll probably stick with the main story first, and add the side stories after, if people are still interested at that point.
I'm only one person, and sadly this isn't sustainable enough for me to work on full time, so the project will take some time to finish, regardless of how I tackle it.