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Taxonomy questions

I have a few questions about taxonomy, both dinosaurian and otherwise,
and I'm hoping somebody here can answer them.

Over the last few months, I've done a lot of reading in both textbooks
and regular books about vertebrate evolution.  I keep running into an
idea that I simply don't understand.  Basically, it goes like this:

The writer describes taxon Y, then says its ancestors probably lie
somewhere in or near taxon X.  However, the writer then says something
along the lines of "no known member of taxon X can be ancestral to taxon
Y, because all known members of X have one or more specialized features
that no member of Y has."

I don't understand why this is a valid piece of reasoning.  It's almost
as if the writer thinks that evolution can add such traits, but not
remove them.  Yet we know that genetic variations can restore features
turned off long ago, as in the hoatzin's wing claws.  And that ancestral
traits can be secondarily lost, as in the cheetah's semi-retractile
claws.  Yet I keep seeing cases of species X eliminated as a possible
ancestor for species Y on the strength of one or two traits present in X
but not in Y.  This just flat doesn't make any sense to me.

Second question: how does one decide what is and is not a taxonomically
significant trait?  I keep seeing statements that species A was
established as different from species B based on a couple of differences
in measurements, or on the presence or absence of a single bone
feature.  Even more common are cases where something that sounds to me
like a minor difference in a bone's size or cross-section is used as a
significant autapomorphy in a cladistic analysis.

Is there something I'm missing here?

-- JSW