I am not sure what programming language renpy works with or what the framework limits you with, so I cant be sure to know what to do (sadly).You realize that story elements aren't the only things that require variables, right?
In general, you could plan the future possible content for some planned versions and set aside the variables. (not that you are forbidden to revamp the program and break saves)
For example, you can generate a list of characters and events for each place, you can then add and work with them without adding more new variables. If you add something, you can initialize them all with standard values.
In my head, this could help a lot if the framework gives you the freedom to do so.