If you had a choice of a server to install Exchange 2013 on, you would want to go with Server 2012. But remember, that decision may have a few learning curve bites to it.
Exchange 2013, the latest server messaging application from Microsoft, has the ability to be installed on either a Windows Server 2008 R2 SP1 or Server 2012 system. So you can choose either. But when you look at the list of prerequisites for each one (listed here: http://technet.microsoft.com/en-us/library/bb691354(v=exchg.150).aspx)you may find that Server 2012 can be ready to go with just an easy PowerShell command that is already put together for you (just copy and paste) and three pieces of software (the UC Managed API 4.0 Core Runtime 64-bit, the Office 2010 Filter Pack 64-bit and the Filter Pack SP1). Installing on Server 2008 R2 SP1 requires several additional pieces (like .NET Framework 4.5 and Windows Management Framework 3.0) along with a few KB installations.
So, it might seem like a no brainer to go with Server 2012. After all, you have to use a new server anyway (being that you cannot perform an in-place upgrade to Exchange 2007/2010 servers). And the new server might as well have the latest and greatest server OS from Microsoft right? Well, here is where the bite comes in.
Server 2012 has the same complex navigational system as Windows 8. A new UI (no Start button) with a whole redesigned Server Manager that may have you spending more time trying to navigate and find things and figure out how to make things work on the new server that you could do in your sleep on Server 2008 R2.
However, don’t let that discourage you. We have to learn Server 2012 sometime and this is as painless as it gets. You can still go with a Server 2008 R2 system for your domain controller (the forest/domain functional level can be as low as Server 2003 SP2). So you’re just dealing with a 2012 member server that you have to figure out how to setup IP settings, join it to the domain, run a PowerShell command and reboot (the reboot might be your biggest challenge) and then install Exchange.
There have been some interesting problems with the installation coming up. Many of these seem to be relating to things like Firewall settings, installing on DCs (not best practice), making sure prerequisites are all installed (roles, features, software) and done in the proper order of things. With Exchange 2013 being so new there isn’t a ton of information on forums but it is out there.
In the end, you have options, but Exchange 2013 on Server 2012 is a great way to kill two birds with one stone. Learn to navigate and work with Server 2012 and get your Exchange 2013 environment up and running fast.