i agree with you. i have seen mojoportal sructure. it is indded a good one although there a lternatives. but as a basic idea, that's the way to go.
i have started doing that for the masterpages and related controls and pages .
the one thing that we have to keep making the difference between the sitelayout and theme. we still need to be able to select a site layout (or a set of masterpages) separately from a theme which should be appled to any layout used ...