Here is a link I found that details what traces should be enabled to troubleshoot message delivery.
http://www.cisco.com/en/US/docs/voice_ip_comm/connection/7x/troubleshooting/guide/7xcuctsgpdf.pdf
I made a test call and pulled the traces from RTMT - looks like you can use diag_CuCsMgr_ files to verify that the caller hit the Unity system and then use the diag_MTA__ files to track the message being left and delivery to the users mailbox. To do this you need to search on the users Alias and then track the message by it's MAL Message ID and file name.
I also found some RTMT Perf Mon counter that are usefull for tracking global message delivery stats