The Fruit of Grisaia doesn’t really have a “true” route or “true” ending as such, since the important plot threads are scattered across all the different girls’ stories.
But if there’s one path that stands out as being of particular importance to the overall backstory of the series, it’s that of Suou Amane. Not only does her route give us some insight into protagonist Yuuji’s mysterious past, which doesn’t get explored in detail until The Labyrinth of Grisaia’s Grand Route, it also introduces us to an important secondary character that, throughout all the other stories, is only hinted at.
Consequently, Amane’s route in The Fruit of Grisaia is a good one to save until last, since it provides a good means of wrapping up that game’s story and a pleasing sense of “closure” to the experience. It also provides some important context for The Labyrinth of Grisaia’s main plotline and an exploration of, for my money, one of the series’ most interesting characters.
Oh, and it’s also worth noting, perhaps more than any of the other characters, exploring Amane’s character particularly benefits from playing the 18+ version of the series, for reasons that will become apparent.