That is one of the struggles with using video. The only “built in” option that I can give around that is to set the slideshow so that it doesn’t automatically advance. That way the user has to manually click the arrows or the indicator boxes to switch slides.
That said, if you’re using YouTube or Vimeo it is possible to take advantage of their API and modify the flexslider call so that it will pause when the video API indicates it is playing.
The way to go about that precludes me from building it into a theme. But as an end user, you can make the changes if you want to.
There is an example with Vimeo at http://flexslider.woothemes.com/video.html
There is also a discussion on YouTube with some code at https://github.com/woothemes/FlexSlider/issues/346
The code you’ll need to change is in custom-js.php.
I also had similar request for the foundation theme at https://support.organizedthemes.com/forums/topic/video-slider/ . The custom-js.php is just a bit different so you’ll want to pay attention to the of_get_option vs. get_theme_mod parts as they connect the customizer or theme options up.
Take care,
Bill