The new media uploader is a totally awesome advancement, hats off to @koop and his helpers.
But... there are a few "power-user features" that are now hidden (de-emphasiszed), and alas, this will break certain workflows (hacks?) that theme authors have put to good use until now.
I wrote an in-depth analysis of how it impacts my workflow (basically, I was auto-populating image galleries with the post attachments), and I think the only solution to keep it working is to write a plugin that extends the capacities of the new uploader.
Here is a first basic plugin mockup:
Theme authors, let me know what you think, your feedback is welcome!