Ok, I have some data to share. Here are the results of comparing mysite.com and www.mysite.com in Google Webmaster Tools.
Links to Your Site
www.mysite.com Not found: 1869
www.mysite.com Soft 404: 459
mysite.com Not found: 0
mysite.com Soft 404: 0
www.mysite.com pages crawled per day: 54,499
mysite.com pages crawled per day: 2,298
One of the first things that comes to mind is the number of incoming links to the site stat. About 99% of them use www.mysite.com. Either that or maybe I need to wait longer for more results to come in?
Also, it seems that I have some crawl error issues restricted to www.mysite.com.