I have to say that I'm very surprised to hear that your Exchange Mailbox server is sized with 12 vCPUs and 48GB of RAM for just 1,200 users. Microsoft says that 12 CPUs is their recommended maximum configuration for Exchange 2010. A server with that much RAM and CPU power is likely sized to support thousands more users than you're running.
Adding more CPU than is necessary is not automatically a good thing. Depending on other VMs that might be running on the host it's possible that you could actually make Exchange perform worse by oversizing it. I think there's quite a few opportunities here to resize the Exchange environment and improve performance.
Here are some good links to help you understand the proper way to allocate CPU and memory to Exchange:
Memory sizing: http://technet.microsoft.com/en-us/library/dd346700.aspx
CPU sizing: http://technet.microsoft.com/en-us/library/ee712771.aspx
Also see this one about understanding how database cache affects sizing: http://technet.microsoft.com/en-us/library/ee832793.aspx
If you look at the article about database cache, you'll see that they determine how much RAM to allocate per user based on the amount of messages sent/received per day. Even if we assumed that all 1,200 users send/receive 500 messages per day (almost definitely not the case), you'd need to allocate 30MB of memory per user for database cache. 1,200 users x 30MB = 36GB of RAM. Even factoring in the memory you need for the Windows OS you still have too much RAM in 48GB.
The same is likely true for your CPU sizing, though that requires a bit more math to figure out. I'd suggest taking some time to review the CPU and memory sizing guidelines as it's possible that the system is oversized and that is contributing to the poor performance during backups.
The other suggestions made by Gkeerthy are also worthy of looking into as well as general good practices, though I don't believe this is a storage issue. Regarding the suggestion of switching to a backup product that uses virtual machine snapshots, though, on that I would suggest that you understand Microsoft's support policy before making any changes. Microsoft is explicit that they do not support virtual machine snapshots of any kind on Exchange. The backup vendor may have included application aware VSS writers to allow them to quiesce at the application level, but Microsoft still does not support it. That means you would likely need to consult with your backup vendor as a first line of support if there is an issue with an Exchange server restored from backup.
I discuss that topic in more detail here: http://www.thelowercasew.com/virtual-machine-snapshots-and-tier-1-apps-not-always-supported
Look into the sizing links I provided and you'll likely see how oversized that Exchange environment is. If I had to guess I would say that is a contributing factor to your performance problems.
Matt