IMO it's worth thinking about FET as if Mity has released four separate games so far, titled "Katara Trainer", "Toph Trainer" and so on. It makes more sense that way too, why the hell would you need to worry about the love system's variables that Azula Trainer had when that game was finished years ago, and you're now working on Korra Trainer. Similarly, why the hell would you go back and work on the mooselion game in Katara Trainer to fix some minor bugs when you haven't touched it in years and the next update of Korra Trainer is eagerly awaited by the fans.
Modularity also comes naturally to things like minigames, since what you're doing on the Ren'Py level is effectively telling the system "go run this thing, and once it's done we'll continue things back here". You could even go on the Lemma forums, find a complete minigame that somebody else wrote and integrate it into FET with three lines of code and about fifteen minutes of work. The logic of e.g., a crab battle or a poker minigame has nothing, and SHOULD have nothing to do with the actual flow of the game, or the map system, or the day night cycle, or whatever else. At most you'll be displaying some porn scenes or setting some variables like the player's money.
