Regarding plants, your trees based on RNA seem to pretty much confirm
traditional taxonomic ideas, e.g. gymosperms, monocots, and dicots are
recovered.  Why shouldn't a simpleton like me see that as clear
evidence of traditional monophyly?  How much do these twin facts
matter?

1. The divergence time of two modern groups is not going the same time
as the acquisition of the traits that define the modern group.  E.g.,
crown group "reptiles" (anapsids I think) and crown group mammals
(synapsids) *diverged* millions of years before the mammal branch
reached anything approaching something we would colloquially call a
"mammal."  (Thus, the divergence time will always "guess
early" as the
start time of a group)

2.  Fossils will never capture the first member of a group, so fossils
are always going to be a "late" measure of the origin of a group.

More generally, let's say that the angiosperm state (defined by certain
characters -- cladists would not approve, they'd rather have a crown
taxon defined by extant groups and their ancestors) was acheived
multiple times.  If all of these lineages were closely related to each
other to start with, and all of the resulting extant "angiosperms" have
each other as their closest relatives anyway, who cares?  E.g., we'd
only have something really shocking if half of angiosperms were sister
to conifers, and the other half were sister to some group of ferns.
Late-night rambles, your mileage may vary...
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