I would like to suggest that for the upcoming version of WP to include some way of using the out of the box set of JS that comes with it. In particular, I have noticed WP comes with thickbox (under wp-includes/js) and since it uses it for managing the media library, why not allow the use of it with the [gallery] shortcode? Some ideas:
* Allow the on/off default use of thickbox with all [gallery] shortcodes by default
* Allow user to override the default setting within the shortcode. Example: [gallery thickbox=off]
* Allow the easy use of other plug-ins. I'm not pretending to believe that thickbox is simply the one and only script out there. What I mean is that WP API should (if it is not already, of course) be clean of "hard-coded" lines of code as much as possible in order to avoid redundancy and scripts being loaded. What I mean is, if a user wants to use lightwindow, why have thickbox being loaded every time the [gallery] shortcode is used?
* Moreover, some good documentation on the Codex on how to make use of the bundled thickbox script.
Hope these suggestions are helpful.