Thank you for the great idea. Different/alternative story lines made by fans would be awesome. We have given the chance to players to request what they wanted and I think we had a total of 20-ish requests over the past 4 years.
Aside from that, what you're asking for is incredibly difficult/time consuming to implement. I asked for extra help not that long ago and there were no takers at all. If we had loads of money, the sky is not the limit, but unfortunately that's not the case. Every minute of game play costs us a couple hours of work.
In theory Koikatsu allows for a lot of customization and that will be the best bet for everyone, the basics are not that hard but anything outside from that has quite the learning curve and is a huge time sink. There are incredibly talented people with the program though to put that in perspective we're probably talking thousands max. On top of that, there's quite a contrast in making a single awesome animation/image or requiring hundreds of them to create a mini story.
With enough time I could make some incredible things and they are there in the game but it's not possible to do that all throughout because when making games I'm basically allowed to average about 10 minutes for a single image/animation because any longer and there would not be much of an update.
Currently we're about 90% done for the final update, we're talking at least about 8000 images/animations. When it's finished I'll post an explanation of the how's and why's and what the plans are for the future. That will also explain the hurdles that come with creating games like these and why we decided to move on to another project.
In short: Awesome idea? Yes. realizable? Unfortunately not.