Mostly because the creators see how much work it is the further the game progress, and if you make forks in the story, then you have more work.
Until the last update it was quite linear, so there shouldn't be a problem. In the case of Fountain of Mana: The creator had more problems, because of the different dresses you could mix and match, and then create for everything you could wear in every possible mix a scene. I think they made it too complicated, but nonetheless it's work.
And that's was most creator don't know at the beginning.