When I first started commenting on romance in this game, I suggested that Larian make it so the player is the one to initiate romance with the characters
Most, if not all, other games that offer romance paths for player characters, tend to do this, and they do it precisely for the reasons that we've gone over in this thread – it puts the choice of what content they want to see firmly in the hands of the player, and stops them from unwittingly coming up against something that they'd rather not deal with. Overall, to make sure the greatest number of players are content, I think this is more or less how it has to be – it needs to be in the player's hands, somehow, to signal to the game, first, before the game makes any moves. That doesn't necessarily mean that your character has to be the one initiating with the NPC, not necessarily... but the player should, either through their character, or through some other above-game means, flag to the game what they want or don't, before the game makes any definite moves at you.
I'm imaging a conversation where, you know, you're getting to know someone before diving into their bedding... and you're chatting about your pasts and your histories and at some point in the middle of the on-going chat scene, there's a nice little simple dialogue choice:
1) [Tell Wyll the story about a boy you had a crush on once]
2) [Tell Wyll the story about a girl you had a crush on once]
3) [Tell Wyll stories about some of the different boys and girls you've had crushes on in the past]
4) [Change the subject; you don't want to talk about romance with Wyll]
And now the game knows what your character wants, while at the same time giving you the chance to flesh out your own character more within the game space. In fact, this kind of conversation is perfect to set up in intro sequences – prologues where you can chat with throw away NPCs that your character is presumed to know (a training academy, a town fair, a harvest festival, etc., pick your trope), but which you use to define yourself, and to tell the game who you're playing, in a subtle, in-universe way.
What if our brain worm didn't just make us build a blank physical doll – what if they put us in brain hack space that was built out of our own memories that we can define elements of, and tell the tadpole all about who we are and what we like unconsciously, and tell the game itself at the same time? Wouldn't that be better than a blank creepy doll?
It starts in haze, but through dialogue choices your recalled to memories of your origin, picking from a few options, and then, memories of a specific setting, building from a few more; it's still vague, but you fill in details as it asks you what you're remembering ,and it sets things up behind the scenes as you go. Maybe it's not quite right anyway – the parasite is building things form memory fragments that it's gleaning, so even details that are personally wrong for your imagining of your character can be excused in this space. The memory serves as a way of teaching the player the basics of playing the game through whatever brief scenario they design, likely without combat, since that's what waking up on the ship will be for later; you'll be able to subtly tell the game many things about your character as you see them, and what they like and don't, and the sort of person they generally are... and then a the end of the memory story, the world breaks apart and cracks, and you're violently awoken to the crashing ship... only now the game knows so much more about you to work with later on.
Sorry got a bit carried away there. I like that idea a lot...
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In terms of NPCs initiating, as they do right now... if that can and will happen, then it need to be smoother; having your character actively hit on can feel weird and uncomfortable, especially if the NPC doing it is highly assertive in the act. A lot of folks don't want that, and don't want to have to deal with it in their fantasy video game. At the same time... I don't think there's anything specifically wrong about a character, if they are so inclined, at least 'checking' if your character would be interested. Gently, respectfully and politely. I think Wyll should, for example, be able to check if your male PC would be interested... but, most importantly, it should be something that he asks without expectation, and in a respectful way, and then, if your character is NOT into that at all, Wyll doesn't act like a disappointed puppy or or take it poorly – he just settles it with nothing more serious than an 'ah well', and, most importantly of all... your existing bromance remains utterly unaffected and unchanged by this after the fact – you've both learned something about one another; you that he is seemingly bi, and he that you are not interested in other males (or even just not him specifically), and that's all there is to it... the game needs to go on as if the romance flag had never been set in the first place, because it was not.
Turning down someone for romance or not being interested in them in that way should never, absolutely never, sabotage your ability to share other close bonds with them and build other non-romantic, or non-sexual intimate relationships with them over the course of the game.
My own perspective may be a little insensitive on this score – from the moment I first began to appreciate other people as giving me interesting thoughts and making certain places feel certain things, I have always appreciated the differences and varying appeals of just about everything... so for me, I don't actually know what it's like to turn someone down specifically because they are of a physical sex I don't like... I don't imagine it's that different from the plethora of other reasons, though, nor any different than being propositioned by someone who is a screaming, blaring “No, Never” to my other senses (which I've ample experience of, believe me)... but I don't actually know, so I'm sorry if my stance on that seems too off-handed.
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I actually really like Ragnarok's suggestion here, about the NPCs having canonical preferences that alter how they react and respond, while still ultimately being open to being pursued. It think that's the kernel of a really good compromise.