Kendra Little explains when upgrades can cause performance to suffer:
The cluster’s servers and SQL Server configurations were built to be as close to identical as possible to the previous instance (memory, cores, disk, maxdop, CTP, etc).
After the migration, I noticed that CPU utilization jumped from the normal 25% to a consistent 75%.
I did several other migrations with similar server loads with no issues, so I’m a bit puzzled as to what might be going on here. Could the upgrade from SQL Server 2008 R2 to SQL Server 2012 simply be exposing bad queries that 2008 was handling differently?
Kendra goes through a number of reasons, building a troubleshooting guide in the process. This is a great read.