Spaghetti programming ftw.
I doubt we'll see legacy moves intentionally come back in this manner. Some of those moves went legacy due to main series incompatibility issues and who knows why other moves go legacy?
Depending on how PvP shakes up Mewtwo may still be potent without Shadow Ball. In main series competitive formats Thunderbolt and Ice Beam (referred to as "bolt-beam") lets a Pokemon hit literally any type for at least neutral damage. Mew and Mewtwo are the only two Pokemon in PoGo that have access to both of these moves and the ability to unlock a 2nd permanent charge move will let them wield both simultaneously. Obviously Shadow Ball is superior to both of them but now people that missed out on Shadow Ball have a solid alternative for PvP.