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Just like Windows Server, System Center gets an updated edition, too. In this section, we detail what’s new for System Center 2016. The core focus of System Center 2016 is on hybrid management—how can we manage the cloud natively from System Center, but also how can we use the cloud to
extend the functionality of system center or manage the environment from the cloud. Microsoft
Operations Management Suite and Microsoft Intune are the management functions within the cloud that complement the System Center 2016 suite.

As you can imagine, a lot of what is new in System Center 2016 also focuses on ensuring that we can
support the new capabilities in Windows Server 2016. Also, System Center 2016 is designed to
truly facilitate the software-defined datacenter (SDDC) and gives you all the tools you require to
accomplish this.

Traditionally, System Center was geared toward managing your on-premises infrastructure. This
continued to evolve in the previous versions, and is yet even more of a focus in System Center 2016.
You can use System Center 2016 to manage your cloud environments, as well. For example, do you
want to know the health of your Office 365 Subscription? In System Center 2016, you now can gather this information.

Breakdown of some of the new features in System Center 2016 with respect to their general management areas:

Device management
Windows 10 deployment support
MDM enrollment with Microsoft Azure Active Directory
Access restriction based on device enrollment and policy

Provisioning
Support for Windows Server 2016 Technical Review Hyper-V features
Rolling cluster upgrades
Simplified networking
Shielded virtual machine (VM) provisioning
Guarded host management
VMWare vCenter 5.5 support

Monitoring
Nano Server
Windows storage
SMS-S support
MP catalog improvements
Performance improvements
Enhanced data visualization
Improved Linux support
Improved network support

Automation
Migration to the cloud
SCO integration packs and runbooks
SMA support native Windows PowerShell
Windows Management Framework 5.0
Windows PowerShell ISE plug-in support for SMA runbooks

Self-service
Improved usability and performance
HTML 5 self-service portal
New Microsoft Exchange connector

Data protection
Azure Express Route supported
Shielded VM support
Storage spices direct

Source of Information : Microsoft Introduction Windows Server 2016