I agree that Emacs seriously suffers from "anti-Python syndrome" (or maybe a better term is just "Lisp syndrome") in that there's many ways to do a given thing

I agree that Emacs seriously suffers from "anti-Python syndrome" (or maybe a better term is just "Lisp syndrome") in that there's many ways to do a given thing and no immediately clear "best" option. However, while it may not be immediately clear, I think almost everything you mention here has a "pseudo-consensus" best option. Not something everyone does, but that most people do, and that you're most likely to see recommended as best practice. - You should be defining groups and variables to provide better documentation and allow use of the interface. But you shouldn't actually use the interface to do customization (put it in your personal configuration files instead). The interface is both pretty annoying and disallows documentation of why exactly you're setting certain options. - You use the standard package manager (package.el) and ELPA, MELPA, and maybe the Org repo. There are a few of these which will require external tools of some sort, in which case fair enough, that's an extra step. But that's still pretty standard in my view (although definitely doing that automatically would be great). I don't think I have any packages that require alternative package managers anymore. - Use use-package. No real question at this point. I do agree that themes are in general a nightmare.