You did not mention how the RuleSet is being called.However, if you are using the RES then it may be that the ruleset is being unloaded causing WebSphere Application Server to do a scan and garbage collection.
This would possibly be the cause of the periodic slowdown dependant on your RuleApp size.
To test this hypthosis you can adjust the maxIdleTime setting of the RuleApp to stop the unloading. Set this as a test to 0 to never unload the ruleset and see if it eliminates the slowdown. Be careful with the setting though as setting it to 0 would mean the ruleset is never unloaded and could cause a memory leak.
Test it with 0, if the problem goes away try and determine the optimal setting.
Link to the knowledge center : Knowledge Center maxIdleTime