I can see one problem with converting every nook and cranny theme_ function into .tpl and that is speed. It is related to the number of files loaded, to make matters worse, I doubt that any of the bytecode caches will help with that for heavy duty sites. That is unfortunate, because it is a rather elegant solution, fitted to how drupal works. Having said that, there are possibilities to improve it, depending what are we ready to trade. Caching - to db or a precompiled file full of theme_ functions are just two of the possibilities, you loose dynamism, but for production sites it is not required in the theme layer.

By the way, the changes to the template system are great. HUUGE kudos to Earl and the little helpers for doing them.