I think a way to implement this is to make a system they already have in place more complicated.

As it stands now, FATES are just.... so simple. OH GUYS!!!!! BLUE CIRCLE IN THE NORTH! MOVE!!

If they found clever ways to chain FATES in different spots... made regular mobs drop pop items that spawns a new fate with a real NM in it...

Personally, the simplest and best way to do this is to just make a FATE with one of these classic NMs have a 2-5% chance to replace another face. For example... the Dodo FATE near ale port is just another zerg... maybe there is a 5% chance that instead of Gertrude popping, another Named Dodo (thinking Nekhbet from FFXII) pops that is much harder at that level, has different abilities and you know... ACTUALLY DROPS SOMETHING.

Maybe these fates need to NOT award ridiculous EXP... but maybe the gil and loot will be incentive enough