First off, this is your story, so you have the luxury of deciding how to write it, and the luxury of saying, "I understand your advice, but I'm going to do it this way," to anybody who posts.
That said, I'm in full agreement with Mirage_GSM on this one. He covered most of the reasons. It'll tear readers out of the story, and considering the nature of a lot of the dialogue/route choices, it'll likely do so at a point where you want readers sucked into the story the most. You're building up conflict, the reader gets real into the story, then all of a sudden there's an off formatted block that the reader has no actual input into anyway. It just serves to remind the reader that it's a story, and I think it's best to make the actual text and transmission of the story as invisible as possible - ideally, while you can still do a lot of less glaringly noticeable tricks with the text, the reader shouldn't feel like they're reading words on paper (screen?). The choices in the VN are given to create a sense of involvement in the player. They're directly responsible for how Hisao's story will turn out. But in a written story, that's already predetermined by the author. It isn't necessary to stop the action to display the choices like in the game. They seem to me to be a gameplay mechanic that doesn't make the translation into a written story (unless CYOA). Your fic may be based off of a VN, but that doesn't make the fic a VN, and in my opinion you should use the tools and tricks that best serve the medium you're working with.
If you really want to show that there's some kind of choice, it could just be integrated into the text without lamp-shading the VN style. Have the character struggle with the decision internally, or go over an option or two in his/her head before choosing one and rejecting the rest.
It’s just... it’s totally your choice, man--all you have to do is show them. Isn’t that cool?”
I gaze off into the distance, pondering Miki’s words as they sink in. As twisted as her reasoning may be, it occurs to me that she does have a point. Even though she did it without asking me, it’s clear that her intentions are good--she was only trying to help me out. I continue to wrestle with my emotions for another moment, alternating between distress and relief until I come to a decision.
“Yeah, you’re right,” I say at last, nodding slightly in agreement. I even start to feel a little bad for the way I reacted earlier, “I’m... I’m sorry for getting upset at you.”
Which is exactly what you did here, and in this medium, it reads a lot easier and keeps the reader in the action than something that would look like this:
“But think about it!” she suddenly wraps her left arm around my neck and holds her hand up in front of us, slowly moving it sideways as if gesturing to some vast, invisible frontier, “You’ve got like... all this potential, y’know! Nobody knows you, so you can choose to be whoever you want to be for them! I’m not saying you have to lie or make stuff up. It’s just... it’s totally your choice, man--all you have to do is show them. Isn’t that cool?”
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Dialogue Choices:
A) So you think I'm boring without your help? Nobody's interested in who I really am?
B) Yeah, you're right. I'm sorry for getting upset at you.
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I gaze off into the distance, pondering Miki’s words as they sink in. As twisted as her reasoning may be, it occurs to me that she does have a point. Even though she did it without asking me, it’s clear that her intentions are good--she was only trying to help me out. I continue to wrestle with my emotions for another moment, alternating between distress and relief until I come to a decision.
“Yeah, you’re right,” I say at last, nodding slightly in agreement. I even start to feel a little bad for the way I reacted earlier, “I’m... I’m sorry for getting upset at you.”
If you want to go back later and write neutral or bad endings, I think the best way would be to do it as you said - Title it "If Hisao had X instead of Y" or something, go back to the decision, and write out the alternate.
If you take one thing out of this, though, make it my first line - it's your story. If you find you like having the Dialogue Choices written out, or like the way it looks, go for it.
Awesome story, by the way. I've really enjoyed it so far. Characters are solid, and I like how there's already some conflict brewing between Hisao and Miki. It's never interesting if things are going TOO well. Keep it coming!