This has been discussed a few times and Matt P (the EP) even acknowledged a few months that he would get the programmers to look at it. Sadly nothing seems to have happened and questions requesting an update on both the roadmap and product streams have been ignored. With the amount of content the game now has it is ludicrous to try and operate with just one save slot. I don't necessarily want to be forced to come back and finish a run on one route, because I know if I fancy a change and start a run elsewhere I won't be able to save that without overwriting the other one. If it's not feasible to have unlimited saves or, like TSC, one for each scenario then at least increase the number of slots to 3 or even 5 for more flexibility.
