Previous posts here and here discussed changes to several of Microsoft's System Center 2012 components with the R2 release, that being Orchestrator and Operations Manager, respectively.
The changes to Configuration Manager, beginning with Service Pack 1 in late 2012, are much more significant. Mobile device management is completely revamped. There is support for cross-platform clients running on UNIX, Linux, and iOS. Integration with Intune via the Intune Connector, changes to OSD, "on-prem" management, and more. So much, in fact, that there will be a supplement to the original System Center 2012 Configuration Manager Unleashed, covering all the changes since RTM. Work commenced shortly after the R2 release, with coauthors Greg Ramsey and Jason Sandys, and contributing authors Dan Andersen, Sam Erskine, Panu Saukko, and Kenneth van Surksum. Look for the R2 supplement to be available the first half of 2014.