I may GENTLY slot some new unimportant "things specific characters are involved in" into the story as I add more areas based on beta content to the game. However, this will be limited, and is planned to be possible to turn off. For example, I plan on making a new options page to turn off the Champ Arena and other new areas (simply won't be accessible visually unless you turn them back on) in the next release. This is so people who do not wish to play with the new content can turn it off mostly if they wish. There are some other areas I am planning on adding that probably will SLIGHTLY flesh out team rocket's operations as the game played out. But again...it will only be apparent if you engage with these new areas, and the game will seem the same as original if you avoid entering them or turn them off entirely.
The main feature for the next release is the moltres dungeon meant to be near cinnabar. This of course, since it makes moltres available a lot earlier, will be possible to turn off. Similarly, if you just avoid it and go to victory road, moltres will still be there if you haven't fought moltres in the new area yet.