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I've been messing around with this today and it has so much potential!! This could very well replace both Views Slideshow and Carousel, with some more debugging. For this reason, I suggest you prioritize other features rather than Views Slideshow integration. Frankly, when Flex is working well, I don't see any need for Views Slideshow, unless one absolutely needs a pager. (and this could be done without Views Slideshow anyway) I suggest focusing on the Views style integration. Now a few observations/comments:
1) The back & forward arrows seem to appear outside the slider div until the mouse hovers over the slide, then the arrows "snap" inside the div and appear as they should. This seems to be a conflict between the css in your flexslider module & the css in the flexslider library folder. (.flex-direction-nav, .flex-disabled)
2) In the optionset's "General Slideshow and Animation Settings" you should probably expand the help description for the margin width to explain that the value here should be the margin attached by the theme. (so flexslider can calculate the item width + margin width for proper slide animation) One would first assume that the margin width value is inserted by flexslider, which is not true. These calculations become critical when building proper slider animation.
3) More UI help is needed to understand the "selector" option under "Advanced options."
4) A new help file is desperately needed.
5) Why not provide a couple more optionsets that demonstrate a carousel and thumbnail slideshow? This would also help us newbies understand exactly how to theme critical elements for custom slideshows. I envision using different namespace prefixes to build CSS for several different slideshow styles. (templates) Then, all I need to do to completely change the look and feel of the slideshow, is to select the optionset that has the correct prefix. In this way, flexslider could host many different slideshow styles in the same site. Powerful!!
Here's hoping you can provide some updates to this module soon. This may be the final solution to the slideshow headache. Thanks!