So I was thinking about how to organize the game and I think I finally determined what I am going to do. It will have the branching paths in the framing story and the game will be divided up into 4 parts. How I have it now, is that the first quarter effects if Meshia ends up using the aphrodisiacs to sleep with the king or if you escape her plot. Then you move to the next quarter effecting the next part.
That keeps things a bit more simple, but it means the game diverges a lot later in the game. Since it goes from 2 paths in the first quarter, to 4 paths at the mid point, then 8 and then ends with 16 different endings. I already made sure to change the format to one with a save feature, so that will be in the next update.
That should make it not so bad to get all the endings, since you can save the game right before the game splits, then go back if you want to go down a different path.