The big secret about MVC is that it's pathetically easy, and much easier in Perl than in Java because of the great templating solutions available and the ease of passing data around. (Java's strong typing often leads the authors of Java templating tools to create their own makeshift version of Perl's basic data types.) You are already doing it (assuming you use templates or something for the HTML generation), and there's really nothing wrong with what you have. As you point out, CGI::Application just saves you from coding the switch logic yourself.

Personally, I like to split up a site into multiple applications to keep the pieces small. Editing user data might be one, browsing a catalog might be another, searching another, etc. This keeps things more manageable.

If you want to see how other people have done it, I suggest you look at this page. In particular, OpenInteract is pretty close to what you're doing.