[Materials] [Geometry]
Inasmuch as there's any truth to the issue of some frame materials being "harsher" than others, this is definitely a non-issue for a rider as small and light as your wife. A small frame, with such a light rider, is essentially a completely rigid object.
Flex does occurr in the front fork, which is not triangulated, so fork choice can have an effect on ride comfort, though, again, for a lightweight this effect is likely to be negligible.
Ride comfort is much more affected by geometry, saddle type, and, even more important, tire choice/pressure.