When you have time, please elaborate on this statement.
Well, here's my bottom line on that.
When I looked at CGI::Application, I concluded what I've already said. And then I went off to commit time to make my own framework.
Since I already have CGI::Prototype in development and deployed at a few customer sites, it's not likely that anything I say now will want me to jump back over to some future version of CGI::Application. Not gonna happen.
If you're developing CGI::Application, feel free to steal ideas as you are inspired to do so by CGI::Prototype's design, but any hour I spend working out the differences between the two is an hour I'm not able to bill to my customers to develop the framework they've chosen on my suggestion.