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Does it bother you that most VNs only give you two options when making choices?

A little bit. I like it when games have lots of choices, even if it's just flavor text. RPGs and Interactive fiction have spoiled me a little, in that regard.
 
I'd say yes, because you can tell right away (usually) which way adds love points for the LI and which not.
 
It doesn't bother me to only have two options because I think what is more important is that all options are given equal attention and lead to equally interesting (and thematic) outcomes. That is actually easier to do with fewer options, as the writer wouldn't need to come up with as many variations that they care less about writing. Usually, the story still needs to go a certain way, and it becomes clear that certain options lend better to what is intended to happen, so the other options end up seeming inferior or are forced to unnaturally converge back to the intended events - I would rather all options be equal in this regard, or to have fewer (or even no) options, rather than forcing options that are written worse or detract from the story.

I'm fine with however many options are needed for the writer to say whatever they want to, whether that's having no choices at that point (and just advancing the story linearly), just having two options, or having more. But usually, fewer options (and choices in general) are better imo because the choices are usually more meaningful then, rather than just being changes in flavor text. And stories are usually better if the writer has full control over what happens, instead of the reader choosing an option that ends up negatively impacting the storytelling (because it was just there to have an obligatory choice), which is why I sometimes like it more when there are no choices.
 
It doesn't bother me, necessarily, but when a narrative design scheme becomes so pervasive, it ossifies, in a way. In other words, binary choices feel less like a deliberate decision, meant to convey a certain aspect of the work, and more like the safe go-to, no though behind it. I've seen many interesting choice-making systems throughout the years (Ladykiller in a Bind, despite not being an otome, comes to mind), so I wish otome games experimented more with this.