My theory is that if you made major changes to your site due to last years Google update madness, then you're likely to get hit with supplimentals etc. If your site has remained unchanged for many years, no matter how much spam is in it, it will probably stay where it was.
I disagree with this, and have proof. I completely redid the URL's on two sites in the beginning of March using the same format. One of the sites has been re-indexed correctly and is getting more traffic. The second has dropped off, is mostly supplemental, and gets about 20% of the traffic it use to.