All these years? How many more years would have taken for Uber to revise and correct the save system? I think he is first and foremost an artist, he has always struggled with code and strictly speaking he can be excused for not seeing it needed something better, it's a VN (it's delusions of being a sandbox not withstanding), the number of variables it needs to track are negligible, I agree it would be better reworked (which could potentially fix several of the persistent bugs), but on balance between the amount of time it would have taken for him to actually do the work and the amount of time it takes to do a workaround is significant (another reason you need a mentor, he'd have spotted earlier the false economy of workarounds vs doing the job right in the first place).
But AFAIK he has a actual dedicated coder on the team now, so maybe reworking the save system will be high on his TODO list.