There is a God Eater collaboration weapon set for the game and the unknown origin of the Thorns of Judgement can easily be the origin of a rogue Aragami boss. It can also be used to tease at the upcoming God Eater 3 as well.
The Protagonist and Jack knew each other before becoming Revenants.
We know that we'll uncover the Protagonist's memories during the story, as well as probably Jack's. Given how Word of God has said that they had a deep connection, it wouldn't be surprising that their relationship started when they where humans, before losing their memories.
The Protagonist and Cruz are siblings.
The Protagonist is shown to be able to drink Cruz's blood without becoming a lost, which could be explained by them being related, though we don't know if Gregorio is affected by his daughter or not.
Alternatively, Cruz did something to the protagonist during their meeting.
I am making this guess based on some footage where she seems to be caressing the protagonist, and I am guessing that this is a hint that she did something to him/her that caused them to be able to survive being shot in the heart as well as revitalizing the tear springs. Maybe she did this to further her own agenda.
The Protagonist's death two days before the start of the game hides another secret.
We know the Protagonist got killed two days before the story began (which might be the moment they became a Revenant), and since we know their past is gonna be uncovered, it's likely that something sinister is residing in those lost memories.
Gregorio and/or Juzo will be the true Big Bad
of the game.
Someone, perhaps the protagonist or Io, will sacrifice themselves at the end of the game to stop Q.U.E.E.N once and for all.
The developers have alluded vaguely to Relationship Values
in at least one interview. They've described bonding with characters to be similar to the Persona games. They could just be talking about platonic friendship, but with a cast as attractive as this, one can hope.
Your character is the Successor of the Heart.
The reason your character survives Jack shooting them through the heart
, an attack that would normally kill a Revenant permanently, is because their heart was replaced with the Q.U.E.E.N.'s heart either before or after the attack. Whether this was intentionally done by Cruz, an accident, or the work of a third party is something you'll learn in game.
The incident of Rin's past is the reason as to why she constantly wears her gasmask, even at the home base.
Whatever happened in her past, it is safe to assume that it had something to do with the Miasma, and it traumatized her to the point that she is now afraid to ever take it off even when in a safe location.