One thing that makes me doubt the need to use Separatists is that they are a faction that needs a revamp almost as much as the Nightsisters. As it stands there are 10 Separatists, GG and the two droids, 4 Geonosians, one Sith, One Nightsister and one Scoundrel, and few of them are of any use. They are mainly a group of individuals with no synergy between them. If they did a legendary with them they would then have to rebalance it as soon as the Separatist revamp happened.
People have said that Legendary events require you to have the opposite faction but that ignores the Yoda and CLS events.
There is also the fact that the current monthly character is Talia and the monthly reward is often someone useful for the new event that month so it could indicate that Nightsisters will be the faction needed.
Before Talia was announced the rumour was that the monthly character would be B2 if I remember, its always possible that the original plan was for us to use Separatists but the plan changed. It can happen, originally the Nightsisters were to be one of the factions used for the Places of Power event until the Devs realised that they were just too useless and they were switched to First Order.
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