[JohnFen]

I think your complaint isn't really about perl and bash. It's about knowing your audience.

When writing code that will be used by a particular sort of user base, the code should be written in whatever way best suits that user base. If your users are academics, researchers, journalists, etc. -- yes, avoid anything with complex or obscure semantics like perl or bash.

But if your code is going to be used by programmers or people who are already comfortable with perl/bash/whatever, those tools may be just the ticket.