I think you hit a good example of when perl outpaces bash. If you are writing applications with options, bash is much harder and a lot less clean than GetOpt in perl.

But I still think it's worth it to learn bash. Or more specifically, 'ksh'. The differences between bash and ksh are small, so think of ksh as the subset. (Off the top of my head, the main difference is forking a process during a while read.) At any rate, the reason shell programming is worth learning is because learning shell means learning unix commands. I'm astounded by the number of perl people that can navigate File:: cpan modules but can't write a decent find on the command line.

Also, when you learn both, you get the best of both worlds. Your shell applications can call perl and vice versa. Mix and match as needed.