We upgraded a default instance from SQL Server 2005 to 2012 today. But Components of SQL Server 2005 are still on the server. These includes the MSQL1. folder (it has all the data and log files), Mgmt Studio and configuration manager. The instance now shows it is 2012 version. I am hesitant to uninstall SQL Server 2005 as it may cause problems. Any thoughts? Has anyone come to experience this? Thanks in advance
Any uninstall of SQL Server will not delete the data or log directories used by the particular version.
The reason your data and log files stayed in the same spot is because you did an inplace upgrade. It will not move the databases to the "new" folders SQL Server 2012 would create (eg. "..\MSSQL11.MSSQLSERVER\DATA").
The only issue you could hit when removing SQL Server is with the shared tools (e.g. SSMS, etc.), but since 2012 changed to using full VS it should not cause any issues.