Hi Akshit,
We do recommend to all the customer to use latest SEP version i.e. SEP 12.1 RU1 MP1
Upgrade path would be SEP 11.x --> SEP 12.1 RU1 --> SEP 12.1 RU1 MP1
Actually need to upgrade to RU1 first, then from RU1 to RU1 MP1, to follow proper supported upgrade path.
Out of SEP 12.1 known issues almost all of them are fixed in 12.1 RU1 MP1.
Check following articles to know more about 12.1
SEP 11.x to SEP 12.1 upgrade process graphical overview.
http://bit.ly/sDogRu
Few differences between SEP 11.x and SEP 12.1 EE
http://bit.ly/JpDR3U
Also check this article:
http://www.symantec.com/connect/articles/quick-access-symantec-knowledgebase-articles-symantec-endpoint-protection-121