I’ve forked 10up WordPress plugin template to suit my needs and stick to my personal file and class organization.
The template will create the folder tree as per the original template but will make use of namespacing and autoloading to speed plugin development further.
The created plugin will activate and deactivate but will actually do nothing but appear in the plugin list: it’s really meant a starting point and not a “press a button to create a plugin” thing.
The template can be found on GitHub.