Strongly disagree. Environment variables are, IMHO, best tool for some simple configuration in unix. They match perfectly with behavior of the ecosystem and other tools in it (like unix shell).

Yes, if your OS is some unversal JS machine, then JSON would be better, if it is Lisp machine, then you would use S-expressions, but on Unix machine, environment/args are way to go.

There are two realistic alternatives - config files and arguments. They have each their own niche, where environment is somehwere between them.

Arguments are better for one-shot setting, not for some setting used always. You can use 'alias' to define shortcuts that always add some argument, but that is definitely more cumbersome.

Config files are good for always/default setting, but are too rigid. Changing config files is equivalent of changing global variable in code, it has system/user-wide effect. While i can just change environment in this one shell and it will affect just commands executed from that shell. Also, config files are much harded to be manipulated from scripts, and use different syntax for each tool.

Perhaps the ideal tool would allow every option to be set/changed from config file, environment and argument.