They'd be silly not to pick Sephiroth. It'll make omega a 5-6-7 combo and it'll milk the hype from this being a samurai expansion.
Plus he's easily the most well known villain in the entire series, so it'll be a huge draw. Even people unfamiliar with FF know who he is because of how big 7 was, and XIV as the 2nd largest mainstream mmo has a lot of those players. I know during Deltascape I saw people going "Who's exdeath?" and wondering why we're fighting mobs that look like they belong in void ark.
As for omega prime, it's easy to work around that. He could be 4 or Sephiroth could be 3, they could throw a curveball and give us a 5th fight; they could even just have him fly away without fighting us and keep him around in the story for reasons, maybe he's impressed with you and wants to monitor your progress. He's quite important after all and fighting another [Something] Prime for 3/3 raid tiers is getting a bit cliche.
