I don't think you're leveraging the greatest benefit of CGI::Application which is the parent class.
Actually, I'm leveraging it more than the average CGI::App user. I have a CGI::App subclass that manages my framework. If I have an app, say, a CRUD app to manage contact lists, it exists as a subclass of my framework class, and might have 5-10 instance scripts. Should I have a peculiar version, sure, i'll subclass it and have some particulars, for for a lot of apps only the templates and the names of some fields change. So I reuse the parent class. A lot. More than most CGI::App people, based on my questions in the past few years on that mailing list.
I'm not clear on what you're suggesting that I'm not doing.