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Whatever new features along with system requirements have been added in SEP 12. RU3 that's the difference between SEP 12.1 RU1 MP1 and SEP 12.1 RU3
This is a summary of the feature updates in SEP 12.1 RU3. For full details, read the Release Notes.
- Plug-in support for Microsoft Outlook 2013
- Support for Microsoft Exchange 2013 Server
- Intelligent Updater support for Proactive Threat Protection and Network Threat Protection
- FIPS 140-2 certification
SEP 12.1 RU1 MP1 release notes: http://www.symantec.com/business/support/index?page=content&id=DOC5564
SEP 12.1 RU3 release notes: http://www.symantec.com/business/support/index?page=content&id=DOC6549
Refer this article as well: http://www.symantec.com/docs/TECH163829
If you are planning to upgrade to the latest version then refer the following article.
Upgrading or migrating to Symantec Endpoint Protection 12.1.3 (RU3)
http://www.symantec.com/docs/TECH206823