@CJW I hope most people notice in ZE, I try not to introduce how YOU the character feels. I agree 100% against being told how I feel in a choice game.
@JimD So far you’ve done an excellent job, it’s very obvious what your getting yourself in for and easy enough (though perhaps too easy?) to avoid relationships in ZE 
I also like how you keep the love arcs interesting and fundamental but mostly separate from the main plot. It’s a nice relief between missions and prevents distraction within them. For e.g. it would have annoyed me if my character was constantly thinking about Heather whilst on the fuel run mission. I don’t care how much you love her, you’d definitely have other things on your mind at such a time 
@CJW for ever 10 requests for more romance in ZE, I get 1 suggesting romance is unnecessary (or that they hate it). The way Heather saunters into the room in Part 3 and flirts was seen as too forward by this latter group of people. So, I try to include it for those who want that part of the game and provide opt-out options for the rest. I find as I write more and more of the game, I add specific sections that maybe only 20 people in the whole world may read. It’s a lot of extra work, but in my mind, those 20 people deserve to play the game as they want to. If your character wants to spend an afternoon having a picnic with Heather, so be it
I think my decision to add romance came before we discussed such things on these forums, though of course romance existed in official games. I admit jumping into the writing of such things by the proverbial seat of my pants.
I’m still kind of feeling my way through this myself, but I sort of see a romantic subplot as just another bit of character interaction. I leave the player free to try and improve her relationship with various characters in the story and leave it up to her own interpretation whether she’s doing it to try and form a romantic bond with someone or just to earn their friendship.
In particular, one thing I’m trying to do is spread out the buildup through the whole story instead of just having one “romance chapter”. You meet these characters early on, decide through your interactions with them whether you like them or not (and through your actions, determine if they like you or not), and decide later in the story if you want to try and bring your relationship to the next level.
As for how you prompt the player? It’s easier for more assertive NPCs – you can just have a point in the story where they ask the player point-blank, “Are you interested?” Quieter characters, it might be trickier to prompt the player about her feelings elegantly. I’m still giving it some thought.
@CPFace
I’m definitely in favor of your method of romantic development. There’s nothing worse for me than a big can of “Sudden Relationship!”, unless there’s an actual plot point that explains this, of course.
Something that develops organically over time just seems to have so much more significance. It also gives the PC time to figure out exactly what kind of relationship they want to have with a particular NPC, whether that be romantic, platonic, or otherwise.