EMR = Engine mixture ratio. The J-2 engine had a valve that could control the flow of LOX to the combustion chamber.
The interesting thing about the EMR shift is that even though it took the engines even further from stoichiometric (which would be an 8:1 oxidizer:fuel mass ratio) the specific impulse actually
increased a few seconds. The amount of unburned hydrogen in the exhaust increased, decreasing its average molecular weight and the efficiency with which the engine converted combustion energy into the kinetic energy of the exhaust. That more than made up for the lower combustion power.
Why not just run with the richer mixture? Two reasons I can see. First, the EMR shift was, as Bob says, timed to cause the two propellants to deplete simultaneously; this time was calculated on the fly by the IU based on measured consumption rates.
Second, while high specific impulse is generally a good thing, high thrust is even more important during the early stages of flight when the rocket is pitched up and overcoming gravity losses. As it pitches down toward the horizontal, gravity losses decrease and thrust can be decreased in favor of specific impulse since the rocket is at that time building up horizontal velocity to make orbit. Also, decreasing thrust toward the end of a stage burn can help limit peak acceleration stresses.