I felt like the things you criticise about the sequels (which I haven't read) are already visible in the original. The girls all being in love with Yuuji and his cum/superpowers healing their mental wounds and so on. That there is no harem route in the original doesn't mean there is ever any doubt that he is the harem master.
Grisaia isn't as much a subversion of anime/eroge tropes but rather a darker and edgier iteration. I don't buy that it's supposed to be a parody of certain clichés, as their overexaggeration rarely ever says anything about them. Yumiko trying to kill Yuuji does nothing to expose inherent problems with the "unapproachable heroine" trope or how it's typically handled through way of comedy, it just takes said trope and turns it up to eleven.
If anything I'd say Grisaia imo actually takes the whole eroge formula to its cynical conclusion. There are the incapable heroines, only this time they are total emotional wrecks. The self-insert protagonist is the only one capable of solving their problems, only in Grisaia he is a super soldier because because the development team realised that a high proportion of the target audience reads these stories to play out a certain kind of power fantasy and Yuuji embodies this completely.