Drupal Wrappers is an api module meant to "help" developers do totally awesome stuff. Imagine a module that took all those "PHPisms" and turned them into drupal functions with proper naming patterns and a look/feel just like the rest of Drupal. That's what Drupal Wrappers does.
DotEquals is a clone of Zen with template files written completely in PHP. The normal way to write a template file is in (x)html with php inserted inline for dynamic content.
Inserting php into an html doc makes it very hard to comment the code. In addition, some people find the code difficult to read because the page is structured around html and the large amount of PHP opening and closing tags can be distracting.