Oracle 12C peformance issue - waiting time increased drastically
There are some known performance issues after upgrading to 12c that are related to the new optimizer features. Try the following to see if it corrects your issue. Note that this will turn off these features for now.

ALTER SYSTEM SET OPTIMIZER_ADAPTIVE_FEATURES=false scope=both;
ALTER SYSTEM SET OPTIMIZER_DYNAMIC_SAMPLING=0 scope=both;
ALTER SYSTEM SET "_fix_control"='12914055:Off' scope=both;