Hi,
That is a good question in general. I only know a few people who advocate the *complete* return to older forms of astrology, without incorporating any of the developments that have occurred in the modern period. For most people the question is more about discovering what the earlier systems were, and then seeing whether or not the areas of disagreement can be resolved. Sometimes there are places where the disagreements can be resolved in some way, while other times you have to side with one approach or another. The sign rulership issue is an example of the latter, I think.
I'm not sure that it is as clear cut with the house division issue necessarily, that the use of the older method requires the complete rejection of the newer one. Because of the interplay between the whole sign and quadrant systems in the Hellenistic tradition itself, which you pointed out, clearly there is some room for both approaches to have a place. The question is simply what place each approach can or should have in the system.
The quadrant system that shows up in Valens and Porphyry was the Porphyry system, where you simply tisect the arcs between the degrees of the angles. In Valens this is the system that he introduces for the purpose of studying the activity of the planets within the context of the length of life technique. So, within that context it was used as a 'dynamic' division, which is the terminology and distinction that Schmidt introduced in his introduction to Ptolemy. That paper can be read online on the CURA site if anyone is curious: http://cura.free.fr/quinq/02schmi.html
The real question, and the one that you are getting at I think, is whether or not the dynamic or quadrant systems should be used for topics, which was the purpose of the whole sign system in the Hellenistic tradition, but became the role of the quadrant systems afterward. To some extent this was already happening during the Hellenistic tradition, insomuch as the degree of the MC and IC were being taken into account and given topical significance. This isn't the same as giving the same significance to the rest of the 'cusps' though however.
Ultimately I think that if you are working primarily from the backdrop of the Hellenistic system in general, then whole sign houses will naturally be the only topical system that you end up employing. Just speaking for myself, that one technique (whole sign houses) was one of the main selling points of the system, because of how well it worked in general, how integrated it is into the system at a very core level, and because of how well it clears up the issues that had been introduced into the system by making the quadrant systems the primary means of determining topics. The question of whether or not that was a necessary or advisable development in the tradition is one of the most interesting points raised by the rediscovery of whole sign houses, if for no other reason than it forces a reexamination of the nature and purpose of house division in general.