This happened to some of my new sites but now they're all back. Only the index page was indexed for these new sites for a few weeks after they initially had 50 or so pages each. Now they're all back. I'm speculating but I think quality regularly updated content is now more important than ever. This makes sense given Google's adsense business. I also suspect that properly formatted code is becoming more important. I had noticed that all of these new sites I'd done had a major flaw in the template code. When I fixed that up all my sites were back to normal within a week. Coincidence? I don't know.
The Google shuffle has cut my traffic in half from last week and my indexed pages also dropped. My pages are slowly coming back. I've noticed that pages that have never been indexed, now are. Same old story with Google ... adapt or die.