I updated my 3rd gen iPad to iOS6 immediately when the update came out since I wanted to check out if the increase in JavaScript performance is noticeable (it is).
However, here's why I regret updating: I've been using the iPad as a second screen on my desk to watch YouTube. After the update, I find that the YouTube icon is missing from its usual place on the home screen. After a quick app store and Google search I find out the truth: Not only there isn't an official iPad-optimized YouTube app anymore, but also that it has the disappointing release date of "in the coming months" [1].
I know the actual reason for the missing YouTube app has something to do with the licensing deals between Google and Apple, but as a generally happy Apple customer my perception is that this "update" makes my life harder.
[1] http://youtube-global.blogspot.com/2012/09/introducing-new-y...