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This isn't the only VN series that organically turned into a trilogy or a duology. A perfect example is Akatsuki no Goei. It has an almost identical approach to continuing things to Grisaia, in that the second game is a combination of after-stories and a route that covers the protagonist's past (which is incidentally even more brutal than Yuuji's). The big difference is in the third game, which is based off of the Kaoru route of the first game (non-romantic route). While it has a core story, it has three main routes and numerous heroines, the big change mostly being in what perspective the protagonist sees the story from. As an approach, it has its positives and negatives. Kinugasa Shougo, the writer for Akatsuki no Goei, hates conclusive endings, and it is pretty evident that Shangri-la (later absorbed by Akabei) forced him to conclusively end the main series in Tsumibukaki Shuumatsuron. His resentment came out in spreading the reader's attention across way too many heroines, in my opinion. Grisaia came out later, so I always figured that they learned from the excesses of the Akagoei trilogy when they made Grisaia into a trilogy, focusing on the cast of characters rather than expanding it massively.