Emergency? Why did Jerkico change the shifts then? No half-witted boss would tell his subordinates to change their routines during an emergency situation, only fascitoid wanna-be-bosses do it.
He was a jerk and Riker was right to object and protect his crew from stupid orders that made no sense.
Jellico wanted them to move from a 3-shift schedule to a 4-shift schedule.
That would mean reduced hours per shift, and thus would reduce the chances of fatigue in a stressful situation.
Jellico was right. A man of Riker's capabilities should have been capable of "getting it done" without whining and complaining.