Thank you for using the plugin and for your kind words!
With respect to "the default Media library" and "your plugin Library", rest assured that there is only one library. The Media Library Assistant is just that, an assistant for the default WordPress Media Library. The plugin uses all the existing database and file storage functions built into WordPress.
Your comments about searching by keywords/tags, etc. when adding existing media to posts and pages are right on target. In fact, this feature has been requested before:
Feature Request: Add Media Dialog: Search by Att. Category"
Thank you and question about possible future feature
What I plan to do is add a new tab to the WordPress (3.5) "Insert Media" popup dialog with all of the filtering options up see on the Media/Assistant screen (mime types, date ranges, categories/tags, enhanced search box, author). It's the right thing to do, but it's a significant piece of work that includes Javascript and Ajax elements. I hope to add it to version 1.2, two releases from now.
Thanks again for the suggestion and for using the plugin.