For my uses of nessus, making a separate interactive CLI interface would not help things, since it will not generate nessusrc automagically. My suggestion ( not sure if it is easily implementable ) would be to make a separate program/script that would pull current .nessusrc in, pull current plugin list, find differences and insert new plugins according to some kind of a rule set. A rule set ( as I see it ) would be a set of statements such as ( not sure what actual format would be good ):
enable new plugins enable new dangerous plugins disable "Denial of Service" group disable port 21 plugins may be even something like this disable title =~ /apache/i Just my 2 cents
