Updated: September 16, 2013 : As mentioned in the comments, the September 2013 update for Lync 2013 reverts the System Tray functionality back to the pre-July 2013 update. HOWEVER, as also mentioned...a bug causing issues with Outlook was found and the release has been pulled. They are working on fixing the update and will re-release it shortly.
UPDATED July 10, 2013 : Based on negative feedback from customers, the Lync Product Group is planning on reverting this change. No ETA / Target CU has been given.
As part of Cumulative Update 2 for the Lync 2013 client, the Lync Product Group has made a change that users will need to be aware of.
Since Live Communications Server (LCS) and the Communicator client, the Lync System Tray Icon has always changed colors to indicate your status as it's seen by others (e.g. Green means available, Red means busy, Yellow means away, etc).
Starting with the July 2013 Security Update for Lync 2013 and Cumulative Update 2 for the Lync 2013 Client (not yet released as of this post's writing on July 9, 2013)...the Lync 2013 System Tray icon has been changed to simply be the blue Lync 2013 logo:
It no longer will change colors to show your status. To see your status, you will need to hover your mouse over the icon:
This change was made to align Lync 2013 with the overall Office 2013 design standard for the System Tray icons. I wanted to make people aware of this change as it is something users will see after the July 2013 Security Update is deployed and is a major change in the way the Lync System Try icon works.