The thing is, there are plenty of other ways to show the NPCs as fleshed out without having them mack on each other. Furthermore, though it may not be the author’s intent, it easily comes off as canon when authors pair possible LIs together. It’s like, “if the MC wasn’t around to screw this up, these two are in love!” Which… makes me not want to play.
If you want to flesh them out more, you can have them talk about their interests or something they did without the MC around. Hell, you can even have the NPC-possible-LIs hang out together without boinking or falling in love. I mean, people do do that kind of thing, right? They don’t have to be trying to get in someone’s pants 24/7 or just because someone else didn’t show interest.
Yeah, I would avoid this game like it had the plague.
As for your other scenarios: a meaningless fling is fine, since it’s not really a “love” connection or a real romance. That said, why the hell do I want to read about it in a game where I’m playing the MC? Alluding to it is fine, but if this is made a plot point, I really could care less unless it’s somehow related to the overall plot.
For the poly thing… well, I have no problem with it. In the game I’m working on, there is a pair of ROs (one male and one female) who are really old and have been together for a long time, but there is a thing in the male’s species where there’s a “perfect” soul connection (the female gets it, but she’s not the same race) and he’s been looking for the third he knows belongs with them for a very long time. If the MC so chooses, they can be that third (also this poly is an ace option, so there doesn’t have to be sex, as long as they’re cool with these two canoodling offscreen, but there does have to be emotional intimacy between the three of them). So yeah, I have no problem with that, or with a poly just happening.
The one with NPC-NPC romance at the MC’s behest is also fine. For ROs whose paths I’m not interested in reading, it’d be pretty cool to have, really.
And, honestly, I really do like the idea of the player being able to enter info for a love connection with other ROs in other runs. I may write a quick game of this just to show what I mean and stick it on dashingdon. Because it’s really in my head now.
When you RP correctly, and the author can write characters well, they kinda are. 
Bingo. And I don’t see how authors don’t get this.
Perfectly stated.
Besides, the point of IF and choice games is to give the player some control over things and to offer choices. It’s not about NPC-B boinking or falling in love with NPC-A. If I want to read that, I’ll go read a book where I’m not investing my time making a character to insert into the world created by the author.
I’m not only fine with that, I would like it a lot. That, IMO, is a good way to flesh out the possible LI without crapping all over my other MCs. Although, I do agree with this:
And don’t particularly like the fact that, in some games, if your MC chooses to get closer to their companions, they end up sucking in skills. There should be enough time for both, or at least more of a balance.
She’s part of it, and knows that. And is more than fine with it. Long story short, there are a whole lot of racial customs/beliefs in this world and she’s been around longer than pretty much anyone, so she gets it (and she wants it, too, she just isn’t as sure as he is of “the third” being out there). The two of them are happy, and not lacking. But it’s like… can’t think of an analogy, really, but think about something you think is perfect and somehow it is made better by adding something else. That’s pretty much the gist.
And she would never play second fiddle, lol. She’d kick his ass if he made her feel that way and go find someone else!