This is going to sound a little like it's coming from a support analyst, but make sure you're on the latest PSU and system+agent system patches as well.
Enterprise Manager 13.2 Master Bundle Patch List (Includes Plugins: 13.2.1, 13.2.2, 13.2.3) (Doc ID 2219797.1)
There are also some memory related parameters you can adjust on the agent side. Have a look at MOS note EM13c : Agent Causes High CPU And Hangs The Server (Doc ID 2213714.1)
Hope this helps
i think that will point the thread opener to the right direction. When we migrated to EM 13c we are also suffering from performance issues in Enterprise Manager. Beside the adjustment on the agent side we also had to increase the Java Xmx Parameter on OMS Side.
That would be worth a try.