How to upgrade SQL Server 2008 R2 RTM to SQL Server 2012 SP3 on the same server? We want to upgrade SQL Server 2008 R2 to SQL Server 2012 sp3 on the same server A. The SQL Server 2008 R2 is on Windows Server 2008 R2 Standard and it has six user databases. 

First we will upgrade Windows Server R2 Standard to Windows Server 2012 R2 Standard. Then we will uninstall SQL Server 2008 R2 from server A.  We will install SQL Server 2012 SP3 on Server A and restore the backup of SQL Server 2008 R2 databases. I have script out the SQL Server Agent Jobs and linked server. So I can run after the restore.

There are only four logins. I script out the login too.  

My question is: do I need to restore system databases too?
Unless you have user-created objects in the system databases, I would not try to restore them.

In fact, if you do have user-created objects, I'd script those out and add them into the new system databases as part of the restore process.

Some of the views, functions, procedures, etc. in the system databases may have version-specific code in them, so it's safest to just use the ones from the new version you're installing.