I had a slight problem with the WordPress 2.1 upgrade, that I traced to defect #3669. However even after I applied the patch code from the defect, I still had problems. I ended up having to live with P tags inside my DIV tags. The problem was that depending on how I inputted a DIV tag in my posting, WordPress would automatically add a P tag inside the DIV, but would not close it properly. I noticed it only because it messed up the look of some of my advertisement blocks. The patch fixed the problem with the paragraph tag closing, but to fix my rendering, I had to actually add to my CSS stylesheet code.
Other than this slight issue, the 2.1 upgrade went well. It is even slightly faster than 2.0.6.
Looks like this bug was fixed in defect 4894. I installed the new formatting.php from 4894 and I no longer get P tags inside my DIV tags. Reference the WordPress Support Forum: DIV and Paragraph behavior in 2.1.