I can appreciate the effort you put into this plugin. Personally, I've found no major issues in how the plugin is designed to work (That says a lot coming from me. I make it a point to break plugins).
With all that said, I think there is some room for major improvement.
First: The biggest improvement, which will probably also increase the popularity of this plugin, is better documentation. You need a comprehensive "How To" dedicated to configuring and using this plugin. In the "How To" you need to cover everything in the SETTINGS area of your plugin (which is most likely where people are missing something, if the plugin isn't working).
Second: The easiest way for people to make use of your plugin is by clicking a button from within the WYSIWYG editor for POSTS/PAGES. You should develop a series of buttons, to work with the default WordPress WYSIWYG editor which accomplishes all the major elements, which your plugin can wrap in a lightbox (I.E. BUTTON 1: Insert Video Content, BUTTON 2: Insert External Content, BUTTON 3: Insert Other Content & etc).
In many ways, the awesomeness of your plugin is limited by the usability of the UI.
Third: Your SETTINGS area needs to be more easily accessible, say from the SETTINGS menu in the WordPress Admin Panel.
Fourth: When viewing PLUGINS from the WordPress Admin Panel, you should move your SETTINGS link to below the PLUGIN title instead of below the description area, so that it is more uniform with the way most other plugins work.
I think you would see major increases in the number of downloads and in the ratings of your plugin, if these four things were part of the plugin's feature set.
On a side note, I'm wondering if there is a way to use your plugin to automatically load a light box, on page-load?