It's really all about getting the job done. There really are things that shell is better at than perl. Not to say perl can't do it, just that the shell is better. For example, filesystem manipulation, chaining groups of commands together (either in a pipeline or just one after another). Perl can do that, no doubt. Just that the shell makes it easier.

My vote is to use perl for what it's good at, and shell for what it's good at. Which can include MakeMaker (or Module::Build) for installing docs.