IMHO the shape of the chainstays has very little (none) effect on the ride of the bike, in the vertical plane. The argument could be made that 22.2mm round chainstays vs. 30x17 oval chainstays offer more lateral rigidity, but it is something I have never been able to detect in my bikes.
The rear end of a bicycle frame as a structure is extremely rigid in the vertical plane, due to triangulation. One stay shape may indeed be stiffer than another, but only by degree. The tires and wheels give way more than the structure, and I would contend that the tires/wheels would fail before any detectable "give" occurred in the frame.
Cheers,
Kirk Pacenti
Pacenti Cycle Design
http://www.bikelugs.com