@photocrati Adding my voice, too, and seconding NFWRo’s question about moving away from the concept of “templates”–that’s why I chose NextGen to manage galleries!
I too have written custom php “templates” to manage/display gallery info for a wide array of uses, that aren’t just views–for example, one produces a json feed of gallery image data for use in several places on our site.
My templates are still in the directory you recommended above (/wp-content/themes/[mytheme]/nggallery), and my shortcodes haven’t changed (somewhere else I saw that ‘legacy’ shortcodes should still be supported?).. however, nothing works, and the only documentation I can find is about the shortcode changes.
Please help!