Think a sort of level reset in another shard's the only real way they could make it work, given how well-known and powerful the WoL is in the source at this point. Wake them up in another shard with amnesia (on a chocobo-like carriage if we're feeling daring) or just put the player in the perspective of another shard of Azem while the WoL's out in a coma or something.

Start players off with new versions of all jobs with refreshed kits from then on, while allowing their lv100 versions to be used in past content so the devs don't have to guarantee their viability in old hard content.