Good points, but not something we're immediately going to address.
First of all, remember that Share is currently a V1.x product. It ships as part of Alfresco 3.0 but is still in it's infancy in terms of functionality.
Having said that, the main use case will be for people to use either one client or the other - not both at the same time. Hence the warning across the top of the JSF client when you access space under the Sites root space. Allowing people to be linked all over the Repository we think would prove confusing - how would you display the folder tree, breadcrumb, etc. when you jump out of a Share Site? I agree it would probably be useful to be able to link to documents throughout the Repository, but this is likely to be presented as "Virtual" documents within a Site.
Regarding the JSF client: whilst we're certainly not "end-of-life'ing" it, it's unlikely we'll port all the new Share functionality across, such as nested discussions in your example.
Thanks,
Mike