With so many references to FFV, my initial instinct would be to assume that the mysterious entity sealed within Eureka is ExDeath.

Though since he already showed up within Omega, I think we can safely write that off as highly unlikely. So, I'm inclined to believe that it'll be something unique to FFXIV or they'll combine references and lift something from another game to serve as the mysterious entity sealed away. Perhaps that could be how they justify adding a 'Necron' or a 'Ultimecia'?