I agree, your time is limited, so it's reasonable to first focus on the common route, (or harem route).
And now that I think about it, indeed there are a lot of characters in this game, so writing in parallel each girls full route would require too much time.
Also, I guess it would be very problematic to write a long complete full route for each of the girls after finishing the writing of the harem route, because it may cause a fight amongst your fans, to decide the order in which the girls would get their full routes written. :D
So I think that maybe the better choice would be to make a long common route with many short small brief branches which quickly converge back into the same linear story line of the harem route, in a way, that the player can still feel that his choices matter, even though the story is moving forwards in one direction until the ending. In this way after completing the harem ending you would just need to add short alternative endings for each girl instead of readjusting the full plot for every route.
I can also approve of the nightmare scenes, or creepy mysterious glitch scenes because they add some good suspense to the story, and can also satisfy those players who do not really care about the characters feelings, because they are just only lusting after sex.
Anyway, thanks for sharing this nice game for free :)