Table start/table end templates
Another note on "Template Encapsulation": Yes I agree that the hierarchical way is preferable, but I can provide (anecdotal) evidence that we attempted this design a few years ago (about mw version 1.14) and run against a wall: Templates were simply not allowed to have that much content by the parser, which was throwing error messages. We ended up with a Key Start / Lead / Key End structure (random example: http://species-id.net/w/index.php?title=Fannia_postica&action=edit ).
This may be one reason why Wikipedia-Table templates, provided some lists generated with them are long, often use the serialized version.
Also, I would like to point out, that for all SMW users, Semantic forms strongly favors the serialized version: multiple records (1:n relations) can be conveniently edited that way. While WMF does not use SMW yet, it is very widely used elsewhere.
Thus, while I agree on the preference for hierarchical display, I wonder whether it is truly impossible to find a solution, a kind of virtual hierarchy. I am thinking of providing an ability to extent existing templates with the ability to call a "start nesting" parser function, which nests all further content until the call of some "end nesting" (or the end of the page). This would greatly smooth transitioning existing templates.