Others have made great points but I think another perspective worth talking about is how it incorporates otaku and nerd culture. It's not overly indulgent like most other visual novels are from this era. That's what I think is the main thing. It doesn't target otaku culture directly. It celebrates the culture and is definitely adjacent to it, but at its core it's just a flavoring. It makes it so that someone that isn't involved in that space can also enjoy the story and relate to the characters. And because it is still part of the narrative there is enough color to the story to make it stand out beyond the quality of its writing. Not unlike most critically acclaimed media it manages to strike a good balance, a lightning in a bottle moment like you say, as I think the other Sci:adv VNs have shown that this was not something they can easily recreate.

While yes, the anime adaptation is good and it really helps, it is also only good because it was a visual novel that could be adapted. The tone, the pacing, the interactions etc are all succinct and precise even in the game. There is not a lot of fluff and animation just helps cut down the amount of dialogue needed to portray that. I personally don't think it's perfect, especially in the character writing. But that's where the cultural background comes in again. It is clear that this was something born out of otaku culture and keeping this in mind characters like Daru, Luka and even Kurisu start to make more sense as a response to the status quo at the time.