There's a few reason I don't like environment variables for this: the first is that a random env variable can influence the operation of a program. Do "export foo=bar" and then maybe 30 minutes later you unexpectedly pass "foo". It's also hard to inspect; the output of "env" tends to be somewhat long, and you don't know which the program will pick up on. Flags are much clearer and more explicit.

There's also the issue that typo'ing "foo" as "fooo" will silently fail. Okay, that's a simple example, but some tools have "PROGRAMNAME_LONGDESCRIPTION". Being in all-caps also makes it hard to spot typos for me. You generally want your env vars to be long, so ensure they're unique.