my impression is that Lilisette and Lilith are one and the same, born from the same parent, but perhaps at different times (Lilith seems older), but were meant to be the same person, at least between the 2 split futures.
This actually makes her quite unique because she's the only character in the entire WotG story so far who has made an appearance from both peaceful and wartorn futures.
I guess she's special in that way, which is why she's one of the Champions of Dawn, along with our character.
Theres no reasoning for our character's chosen destiny, tho i suppose its in the nature of FFXI missions to make us become the main protagonist somehow...
LOL.. wouldn't it be interesting to see if Lilith is assisted by an evil alternate version of ourselves?