It’s because git is a complex tool to solve complex problems. If you’re one hacker working alone, RCS will do an acceptable job. As soon as you add a second hacker, things change and RCS will quickly show its limitations. FOSS version control went through CVS and SVN before finally arriving at git, and there are good reasons we made each of those transitions. For that matter, CVS and SVN had plenty of arcane stuff to fix weird scenarios, too, and in my subjective experience, git doesn’t pile on appreciably more.
You think deleting an empty directory should be easy? CVS laughs at your effort, puny developer.