It isn't really that much work although it is a lot of changes, if that makes sense.
What I wanted was more complicated though, so I've made many changes that aren't all directly related to habitable planets. I wanted a more "accurate" mix of star types, more variety in the solar systems of different star classes, less common habitable planets and orbital resources that made more sense to me. When I only reduced the number of habitable planets the game felt resource starved so I then altered deposits so that stars always had something (energy or science) and all asteroids had minerals and that was a very easy change of just a couple lines in the null deposit entry and some weight modifiers for minerals. Once I did that I still wasn't happy with the overall planet distribution so I tweaked the planet types to distribute the habitable planets min & max distance from the star as this allowed me to balance out the different planet classes better since my system initializers were altered to use random colonizable and random non-colonizable planet classes instead of just random classes.
I actually avoid using some of the games built-in odds values (planet & star classes) since I found it easier to control those results by controlling the usage odds of solar systems and then within those systems having more strict planet placement. To do this I have a lot more system initializers than the base game but in reality many of them or just variations of a few basic systems I setup.
In the end my game never has habitable planets in class A, B or M systems so those systems have higher chances of various resources. I also have a few "empty" systems that have a few visual effects (like an asteroid belt with no large asteroids) but nothing useful beyond the star itself. I was also able to balance out the value of nebulae since those are required for many strategic resources I have them setup to have virtually no habitable planets within them. Combine those basic "rules" with the ability to weigh system odds effectively by star class and although I have a ton of different possible systems it's easier to control the overall makeup of the galaxy. Or, as I like to think of it, less random without being more repetitive.
All in all I have about a dozen custom files like "habitable_system_initializers.txt" some of which are a couple thousand lines long but I think it's an easier way to do it than a couple small files with a lot of random variations in them like they did with the default misc_system_initializers.txt file. I also think it's a lot harder to try to explain this that it is to do it