visual novels have some core pillars, the history is in general linear and don't have player input. 

"Thats not true! a lot of visual novels have choices and different  paths! and it uses my input to do it"

yes! my game also have, but what I mean with general linear is: 

this is basically a line, but  I not saying this in a bad way . And chose something is a low effort input, still give the idea that you are doing something but is kinda whatever  

Make a good plot with real path bifurcation that will be consistent for the entire history and nice to read is just delusional most of the time. 

if you have a choice in the middle of the game, for example "do you wanna kill this EXTREME important character?" you need to create 2 different games at this point.

"But, it's like 2 cool stories right? sounds good to me"

Well, making 2 stories 1-ish hour long is plausible. But and the long stories?  you put a 2x work load already, and the longest the game are more people will want another path.

*math some times is cruel*

Developers work around this in a loot of ways, like end the game if a specific choice is made, create a local path that will return to the normal flow state or make a lot the bifurcations close to the end.

What I wanna to say with these thoughts is: I don’t think that big main plot choices moments are a good way to take some input. The bigger they are more limitant the game become. 

But I want options to kill important characters or other cool stuff.

So I will follow the pillars: 

• The player will never make any important choice in the main plot
• If there is a choice in the main plot is a local path that don't change the future because come back to the normal flow or because Sara dies. 
•  Every non-visual novel type in tha main plot can only return death/endgame or success. 
• The main plot will use others plots data to change something or to give advantage
• The player will have a lot of incentive to explore secundarie plots, because is the only way to make the main plot easy.