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.