I have a hypothesis. I think Cassandra will be our secondary protagonist, in the same way that Alistair and Varric were (and to a lesser extent Morrigan); she'll have a role to play throughout the plot as a whole and won't be able to leave, if ever, until the very end. She'll be part of the Inquisition almost as much as the PC is, I think...
And as to why that is? This is more of a guess, but it would seem to me that the Chantry might now be in utter shambles and unable to exert any power in an organized fashion. Perhaps the Divine is dead and there's a power struggle; perhaps only the struggle. Perhaps the templars are taking over portions of the Chantry. In any case, Cassandra might decide to help rebuild the Inquisition solely because it's the only force that might be capable of restoring some sort of order... and, after this, have only hope that this order will include the Chantry.
For players who aren't inclined to side with the Chantry, I'm wondering why Cassandra would be a mandatory ally. I would have to assume that Cassandra would realize that a Vashoth or Dalish protagonist may not be inclined to help the Chantry or the Divine, especially since the player isn't "a puppet of the church" and the Inquisition is created "in opposition" to the Chantry.
I suppose if Cassandra is neutral and no longer tied to the Divine, I can see it not being an issue, but so far, it seems odd to have a mandatory companion who has ties to an organization that the player may strongly detest (which would make her the opposite of Alistair, who was a member of a neutral organization - the Wardens).
Just wondering why the Inquisitor would take her on as an ally. It's not like the main character is going to have the same frame of reference about Cassandra (or Varric) that the player does. If you're Vashoth or Dalish, a member of an evemy organization is basically extending a hand, and I think some would be hesitant to trust that gesture when Cassandra is (most likely) a complete stranger to them.