The added dimension really made things intuitive so you weren't left guessing which vertical had to do with what. One space would give you enough context to know what might be next navigating up/down. It's really a shame how disruptive the change to Mission Control was by removing them.

I tend to organize my spaces by projects and then a dumping ground for "everything else" like general browsing and music.

For projects, unique windows are typically: IDE, Browser(s)

For apps I commonly use across spaces, I assign them to "All Desktops" so they follow me, like iTerm2 and Heynote for keeping notes / task lists even if they cover multiple projects.