Well, I wonder if the issues with the merge aren't about putting all the existing content together, but rather more laying the groundwork for the following content. If I remember correctly the direction of the game is supposed to change from a linear story to a sandbox version. Pick and choose what girls you want to progress, who you ignore, etc. Wouldn't that mean you'd have to code multiple choices of girls, with whatever actions available with them, for each following day, while simultaneously progressing with the intended main story. That would be a lot of information in the save files (I guess).