I use the shadowbox.js plugin for my images and other stuff, and I use the WP2.6 gallery with it. The problem is that I am more prone to typos because of having to make the connection between the image and the shadowbox by hand each time.
Just as the gallery has options for alignment and float and size, it could allow for other options that would apply specifically to plugins like shadowbox. I'm guessing it would be a start to at least make that easier to do, since I haven't been able to find any plugins that offer that integration yet.