The big issue is that the EMALS system is easier on the airframes. In a conventional steam catapult, the steam head hits the piston face at max pressure and expands as it accelerates the aircraft, but max acceleration occurs at the beginning. This means there's much more load on the aluminium components of the airframes. As aluminium has no elastic limit, all deformation is bad. The Navy goes through a lot of airframes compared to the air force.

The EMALS system is intended to spread the load out continuously during take-off so the max load is much lower, thereby dramatically increasing the lifespan of the airframes.