Increasing time to save data is inevitable with a pile of files database unless the world file allows random access by having records of fixed size. This would make the world file bigger, but only records which had been changed would need to be written.

If they are not doing this, but saving the whole world file every time, then save times will steadily increase as you explore and build.

I think they should use SQLite for the database. They would get random-access and a whole lot more.