Completely Understand due to issue of Branching which is a whole other Kettle of Fish and difficult. Don't worry too much about the Agency if it is going to put you into"Feature Creep" which will add to the complexity of your Code and Project in general.
Once you have the Season 1 and Season 2 Build on the same code base maybe you could work out the Carrying over of Stats from each Season or allow the Player in Season 2 to input their Stats.
Keep up the Great Work and your Writing, Pacing and Characterization / Artwork are ALL Excellent!