Not trying to be antagonistic, but it is possible to have a game with hundreds of variables and not start over each release. You're describing programmer limitations, not engine limitations. This is why a story should be written in its entirety, then coded, setting aside variables as they will be needed. But if each release the developer chooses to add or change things based on whims, then breaking saves is the result. I think you will find that continuing in that fashion will necessarily trigger the law of diminishing returns. More and more folks will become irritated which will lead to increased negativity and antagonism in this forum (and possibly elsewhere). My advice is to draw a line in the sand and go with what you have.
You're learning and have a pretty good game in the making, so keep at it, you'll get better.