I've upgraded to 4.1 a few hours ago.
I don't have the collaboration service installed which is needed to configure the LCS and enterprise messaging options I want. I don't see how to install the collaboration service either. During setup when it got to IM, the only options were groupwise or sametime, no LCS. So that is one issue for me.
The second is that I have unity send the .wav vm to users and still can't open the .wav attachment. I understand there is more integration coming out with unity but i'd rather not have to follow a link to play .wavs if I can get it working now just by opening the attachment. I see in the bes now that wav says enabled but when trying to open it says unrecognized doc format. Doesn't seem like a sampling issue.
So those are my two main issues, otherwise the upgrade went smooth and everything is running as before but I love the new interface over the legacy mmc one.