IMO Love Interests should be clearly identified at the start of the game: "Alice, Bea and Carla are the girls you're going to pursue. The others are just side characters."
This is something that devs too often tend to forget: it's been a while since launch, but they have designed this new character that's so much more interesting than Alice, Bea or Carla and they start giving her love, at the expense of the original three LI. This causes confusion, and confusion causes contrasting expectations that can't be all met.
NTR isn't as clearly defined as it looks: in the end it's all about creating jealousy, that's subjective.
If in making a non-netorare game the dev doesn't make a clear distinction "these are the girls that you will have, the others are free to pursuit their own life" you can bet that he will end up pissing off
royally not only the irrational wannabe-sultan crybabies (that are better lost than gained anyway) but also most of the normal players who just happen not to like netorare, like the ones posting above me. It's not like there's a shortage of lewd games to migrate to.
Why devs all too often end up straying away from what
Larry2000 called a "Wholesome Harem story" is actually pretty easy to understand.
Tthe most common reason happens when, as above, after months or even years spent on their game, a dev ends up feeling that their story has gone stale. The original driving conflict (that too often wasn't more elaborate than "try to get laid") lost its strength, so they might decide to introduce a new conflict or spice up the story. And they think: what better conflict than "Hey, now you've got a rival!"?
Or maybe they grow disaffected with the MC, so they introduce a new bull that they feel is more interesting.
Another reason is the lack of the knowledge that players self-insert in the game and identify in the character. Not many understand this, as it happens mostly in specific game genres (compare, for example, FPSs to strategy games).
So a newbie dev can just think "Let's give players more sex scenes, some with the MC, some with this other guy, and there let's give a nice gangbang to the main female lead."
Newbie devs ofter have porn movies as reference for deciding what's hot in lewd media: newbie mistake: they are different medias and are percevided differently by their fans.
This most often is the cause for the dreaded ntr-mislabelling at the start of the game: a newbie dev often doesn't think that the MC should feel jealous in that situation. They aren't jealous, so they wrongly assume the player won't feel jealous.
Drama usually ensues.
Those reasons usually stem from the original idea of the game not being more elaborate than "Let's write a Harem Story: they're very popular. OK, so let's have this young guy... let's not make him too much of a loser... and now let's put him in this kind of situation. It's [original]/[popular] enough, I bet this one will be a success, let's start and then I'll think about what happens next."
On the contrary, when you develop a game, you should have well clear a story with a beginning where the characters and the situation are set up, a central section where the stuff happens and an end where we see the consequences of the stuff that happened and the story gets its finale, that's the point you're trying to make (yes, even in a porn game! "And he flew to a land where polygamy is legal and married all the girls of the harem" is making a very clear point, after all, isn't it?)