Good points, some of which can be addressed:

Re: conditionals SGML allows marked sections to have parameter entities as keywords, and recognizes INCLUDE/IGNORE in their expansions:

    <!entity % e "include">
    ...
    <![ %e [
      will only be included if
      e expands to INCLUDE
    ]]>

Re: mixed user/system text SGML supports quite restrictive content model exclusions, eg the "-(script)" part below makes SGML reject script elements in main's content anywhere:

    <!element main - - ANY
      -(script)>

Moreover, you can declare an entity as a so-called data text entity, special chars in which are preserved

Re: running legacy parts There's no difference to what PHP does now eg just running through the page/template doc until the end, erring out on validation errors?