I agree with most of what you said, and you helped clarify some of my own thoughts. The MC returning home should have been huge, and nothing was done with it. The reunion with Tara should have been huge. Even if the devs didn't make her a love interest or have a possible trouple with her, she was a huge part of the story, and there should have been a pay off and resolution. Whether Amanda was involved with Mallory and the MC had almost no impact on the story. There should have been scenes that addressed that situation if it existed.
I had exactly the same problem. I ended having to go back almost to the beginning and changing the two times I said I was interested in both, during the topless sunbathing scene and before shots at the bar, to focusing on Jaye.
I had two saves at the end of chapter 8. One with Jaye at max love and trust, and one with Mallory at max love and trust. It was impossible with either of those to have the chosen girl have max points at the end of chapter 9. Ironically, I did end up with Mallory exceeding max points on the polyamory route due to the massive boost she gets when you agree to it.
Anna from To Be A King was made a cameo in this game. Jaye, Mallory, and George made cameos in Single Again.
My first ending was dying on the boat to the assassin. Why? Because I didn't train with Tanaka. Why? I didn't want to cheat on the other girls.
As I mentioned, the last two chapters felt rushed. The threat just escalated with the attack. The characters just learned the true extent of the threat and that they were being targeted directly (we as players knew much more than the characters did due to the various scenes away from them). And everything was resolved in chapter 8. Not a single decision you make in chapter 9 impacts the threat. There are two virtually identical outcomes with minor variation in text. Far different from the different paths you could take earlier in the game. The trust stat is almost worthless in the last half of the game. You'll get penalized trust points for cheating, but trust points are never used to determine any outcomes. If you sleep with Lisa while in a relationship with Jaye, she'll resign. If you try for a committed relationship with both Jaye and Mallory, you get a bad end. Other than that, there aren't any consequences for cheating. A lot of side characters were sort of forgotten. It really does feel like the devs just decided they were done with it and rushed to the end. Hopefully, the epilogues will help, but it did hurt it. This game went, in my opinion, from being a good game to just above average.
It also didn't help that Mallory and Jaye were the main love interests, with Jaye being the primary. Don't get me wrong. I liked Jaye, but I liked Mallory better. And I liked Lisa as much as both of them, and she felt like she deserved an ending. I liked Bianca a little less. And Tara was such a big part of the story that, relationship or not, sex or not, she needed a few scenes towards the end. And Amanda needed specific scenes if she was part of the relationship with Mallory. And I wanted to know more about what was going on with Erika and her family.
Actually, I think I just realized part of why I feel this game became disappointing. Just like it seemed like the devs wanted do something complicated and grand with the routes and stats early and gave up, it feels like the devs didn't know what to do once the characters were in relationships. Jaye and Mallory were more interesting before the MC got into a relationship, open or committed, than afterwards. Variant scenes mostly vanished. A couple of sex scenes. It's like they didn't know what to do at that point and just wanted to wrap it up. The game feels like it got smaller and simpler as it progressed. I may be entirely wrong, but it just feels that way to me.
My guess it that you will have an option if in an open relationship with one or both girls to commit to one before you get set on the alone path.