The project I've been working allows a theme developer to adopt bootstrap styles. One thing I don't like about bootstrap is having to subject the markup to bootstrap's classnames so I drop in bootstrap styles through mixins instead.
Especially all the grid related class names don't seem elegant to me for building a WordPress theme (fine for a quick mockup/early stage site though).
Let's say you want to have a wider sidebar, you'd have to change the php template file when it should be a simple tweak in the css.
- Manual loading of jQuery, will lead to multiple jQuery loaded
- Missing apparently all action hooks, see wp_head(), wp_footer() etc. This breaks basic blog functionalities and many plugins.
Not good:
- Hardcoded path to CSS files, see wp_register_style etc
- Hardcoded path to JavaScript files, see wp_register_script etc
http://codex.wordpress.org/Theme_Development would be a good start.