You do bring up a good point about the meta reason for NTR. I can't count how many games start out promising, but peter out until they either cease development, or come out with a product that isn't what was advertised.
Netorare isn't my personal kink since netori is more what I enjoy, but I would agree that a lot of NTR stories don't fully understand how to capitalize on the NTR aspect. I find that too many games lean on NTR solely being a "kink," rather than NTR being a genuine part of the story process, which is why I feel it sometimes ends up being diminished over the course of a story. And while that isn't bad (as a lot of fetish content does this as well), I am always interested in how stories can be improved or crafted differently.
What stands out to me in Fujino's story is that NTR is used as a device to reinforce the themes of the main couple, rather than just being a kink.
For example, not only is Inoda going after Asuna, he corrupts the mother as well. This emphasizes the "power" Inoda has in real life compared to Kirito in-game, who is subservient to Asuna's mother. It forms a hierarchy in which Inoda is at the top, while Kirito is at the bottom. It also serves to show that Inoda is capable of eventually corrupting Asuna, considering he has done so with her guardian.
You could also see his constant corruption of Asuna in the game as a slow usurpation of Kirito's raw combat strength in FOG (which fits the stealthy, crafty, rogue-type personality that Inoda is displayed as, as opposed to Kirito's blunt, awkward, and brute-force way of doing things).
Suguha gets corrupted by NTR, but that's used as a way for her to pursue her brother. Liz uses Inoda's plan to steal Asuna as a way for her to get with Kirito, which then serves to throttle Inoda's relationship with Asuna. The activities with Alice are used as a device to sow doubt within Asuna about Kirito, while also doubling as NTR with Klein. The story doesn't stop at "Inoda cucks Kirito," it uses NTR in very creative ways from normal NTR games I've seen, at least in my opinion.
This could also just be me talking out of my ass and me being completely wrong about Fujino's story, that is just as likely.
I think one of the changes I disliked about Fujino's story was the decision to stop including NPC sex scenes in the game (even though I think it was necessary in order to allow Fujino to focus on the other characters).
The NPCs in Fujino's previous games, as well as Part 1, were a great way to implement NTR into the interactions of the city, because they reinforced the state of Kirito's mentality throughout the game while also serving to populate the various areas. That green-haired guy who indulged in NTR with his wife in the church was a great marker as to where Kirito could be at the end of his journey, almost like a foil. There was an entire sequence where you needed to talk with him, so it was most certainly done on purpose.
And while these NPCs still exist, they lack a purpose. I used to interact with these NPCs in Part 1, but in Part 2 I rarely do after the change to stop including them, because their current interactions are generic. In his Scathach game, the inclusion of a sub-heroine and NTR within the village made exploration much more rewarding.
Sorry for the wall of text, I just talk a lot.
