I think that the biggest plus in favour of CGI is wide distribution and user base. It is pretty rare to find a perl installation that doesn't have it, and of course it is the de facto standard for CGI scripts.
Something like CGI::Simple means a good chance that the user has to install it. This is something you need to consider, particularly if everybody starts using their favorite CGI::* module instead of the standard CGI.
I might consider using one script over another if that script used modules I already have, rather than ones I need to install. (And of course, some don't know how to install modules, or don't have access to do so.)
This is not to say that CGI is the best or only solution, but these are things that I think also merit consideration when deciding what module to use.
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