We librarians think that the best solution would be to have 3 main repos.
One repo for all footprints, one for all symbols and one for the 3d models. (Would help us organizing pull requests.)
In addition a few smaller support repos will be needed. (3d model sources, templates, helper scripts, ...)
But this is far in the future. It is guaranteed that v5 will keep the current footprint mess.
Another thing to remember is that the 3d model repo is quite large (data size) compared to footprint and symbol repos.
Why can't the 3d models be in the footprint repos?
Well the github plugin downloads the complete repo every-time it needs any footprint information. (As a zip file, not via git) If we put 3d models in there, waiting times will go through the roof. (This downloading is the reason why starting cvpcb takes that long.)