|Don't ask to ask, just ask|
The oddities in Perl are more or less documented for the most part and also is reverbrated across FAQs, their behavior is consistent with Perlishness, I am not standing in defence of that, however, once an odd thing has been spotted, it will be remembered and gradually it will start to make sense, something like scalar keys %$some_hash or the list and scalar contexts behavior of certain functions.
I was actually taken aback by the statement on the validity of Perl as long as Bio data is in text files that I missed the string processing and the very nature of representing DNA and protein letters in string, that was a good point ELISHEVA
Perl friendliness can be a weak spot that outsiders take to accuse the code as being unreadable and clumsy, I was able to learn and get started on Perl quickly, but not until I joined the Monastery did I shape up my coding and stopped shaking, and of course, I am yet a novice and yet picking things up to stability, the point is, friendliness allows those wanting to learn the language to quickly pick it up but doesn't guarantee that they can write the cleanest of code out there...
raybies have a good point with all the requirement for the Visual component to gear up, but, well, Perl can be part of a production that depends on visual orientation, in my line of work, there's this CLCBio suit of programs specific to sequence analysis, some of these programs are Perl modules and the entire thing is wrapped up in a very sophisticated GUI interface. STATPerl is another one, the author has made All analysis and graphs in perl, only the user interface is developed by VB6 and I have seen some Tk/OpenGL marriages, but of course, thinking of building a GUI and then plugging code into it may not be a joy-ride in Perl as compared to Java Applets for example.
Regular expressions can go nightmarish, when they do that YAPE comes into mind, compared with other languages that do regexes, Perl stands out because of its inherent text processing capabilities, so having an engine to parse patterns just completes the entire toolset. If someone did not invest the right amount of time on learning Regular Expressions in an incremental progression they won't accuse themselves for the cause of their inability to understand and employ regexes which, in part, is not fair, they are cryptic but that's their nature and that's their coolness..
I oft refrained from wading into bickering arguments and always entertained the opposite opinion by forgiveness, for those who do not know can be forgiven since they do not know but once they know and go overboard on their attemtps of attrition, you tend to lose your cool, the emotions for Perl are always mixed, there are those who just love to hate the language as bellaire says, check the Urbandictionary's Perl entry. While our love for the language should not blind us from identifying weaknesses we still do not seem to have the habit of picking on other languages, which is really supreme on our side and this is one of the reasons that this community is so vibrant and so focused.
Perl looks natural as a language more than SAS for example, it has fewer constraints when it comes to typifying variables, a number or a string are efficiently dealt with, the memory management is automatic, the TIMTOWTDI rules over Python's deterministic approach and many other qualities that shall make this langauge last longer than perceived
Other source of confusion that causes some to predict the demise of the language is the Perl6 counterpart (so to speak), many think it is a replacement to Perl and they go the extra mile of saying this and that about the counted days before Perl becomes obsolete, that shakes the confidence in those contemplating spending the time and efforts learning Perl or acquiring Perl into their stash and serves an empowerment deal to those who wrongly choose to hate Perl.
In conclusion, my plattering should've been titled "What's it with those who hate Perl", and I should've tried to look into their genetics for clues... :P
Excellence is an Endeavor of Persistence. A Year-Old Monk :D .