> 
> 
> Personally I would like to see <sep /> for lists as well at the same
> level as <li>
> 
> <ul>

ul lists are sets not sequences, so there is no well defined position for
the sep.

> Tree hierchies make for lousy document modeling of everything but the
> overall document structure. They don't work well for character styles

I'm not convinced that they do in well structured documents, although it
does seem to be the case that early Netscape browsers parsed separate
trees for each type of styling markup (i.e. turned on on a non / tag
and turned off on a / tag).

> (they often overlap) 

Most of the structure clashes that I see are the result of trying to
impose a layout that doesn't have the same structure as the document.
Tagged PDF deals with that by having inline markup where the structures
align and dividing the rest up into the intersection of the two structures
(structure clash resolution in popular 1990s programming methodologies) and
using separate tree to represent the alternative structure at that level.
PDF, of couse, uses presentation for the primary decomposition.