Christopher, the responses you interpret as snide to questions about
neo-darwinian theories are not dismissive, just exasperated.
   Take any currently accepted theories in science-- you mentioned
relativity replacing newtonian dynamics-- and the same criticisms can
be found.  In a few cases, the criticisms are of sloppy wording or
thinking, and are useful. Others have agendas that make them not
amenable to serious discussion among specialists in the area
questioned.
   You can find books published decades after Einstein's 1905 and
1915 work, refuting to the authors' satisfaction many aspects of
special and general relativity.  Occasionally someone took the
trouble to point out the assumptions and false steps made in those
books, only to find the same arguments cropping up as though the
effort to reply had not been made.
   Asimov took quite seriously the question of whether it behooved
those in a science to pay close attention to the Velikovskys in hope
of finding a neglected truth. He concluded that it did not, because
there were so many notions to look at, that it made more sense to
continue work and seek improved formulations directly, not via
philosophy or messages from beyond science.
   The short answer to doubters of neo-darwinian ideas is, set up
experiments to demostrate what's lacking. Waddington did it, on
inheritance of acquired characreristics, and his efforts were and are
taken quite seriously, and form a small but significant part of the
current picture.
   So take specific cases where the consensus seems unable to account
for an event, and give some alternative explanations that can be
tested against whichever current model you don't like, including
punctuated equilibrium if that too is unacceptable.
   The shortest argument against directed evolution is the
Argument From Imperfection: a Director of Evolution must be quite
ignorant or quite inept to have made so many false starts,
backtrackings, and wasteful byways.  The resulting movie is virtually
plotless.               Pet