That's a good question. I've emailed Lincoln asking about his thoughts on CGI v.3; my assumption is that he does recommend it, since he calls it CGI.pm version 3. However, he also added new features to version 2.
This was the response I got back from Lincoln Stein:
Actually I've scheduled version 3 to be removed from CPAN altogether.
It has too many bugs for production use and although many people send
me bug reports, no one has volunteered to help me fix them.