Not all plugins works well out of the box. Some plugin require a theme support, from simple CSS tweak to template files modification.
As a theme developer, it’s hard to choose which plugins I should support in my theme. It takes time to do this, and theme developer also need to “watch” these plugins to make sure all is working well for latest version of each plugins.
Popular plugin such as WooCommerce also have large user base, and it can increase theme popularity. So, without further ado, here is the list.