We need to create a naming style guide & structuring hierarchy objects. How do we structure Environment objects, be it Trees, Houses, Cities, Forest. Same goes for managers, other objects and their parents.
This is important because the hierarchy will get messy quickly, the sooner we will do it, the better.
Trees inside Trees folder, Houses in Houses, Cities in Cities? No? 
I’m working on tool that makes organization and visual hierarchy orientation much easier:
https://github.com/neon-age/Smart-Hierarchy
It needs customization support before we can PR it into project
Honestly, I’m still pleading for actual official folder support in the hierarchy instead of empty GameObjects, but seeing as this isn’t the place to complain about that, I’m seconding @Neonage 's suggestion.
Also @Neonage , that looks like a really neat tool. You plan on keeping it available after the project’s done?
I’m planning to evolve every tool I make, cause I use them in my own projects as well
I’ve been waiting it for ages, and it’s still non even in 2020.2 beta, so i’ve made it myself in one day 