If I remember correctly, someone from Bioware (David? Mike?) mentioned that at the point in time where Cassandra is interrogating Varic, the Chantry is in in a very bad position - perhaps even on the verge of collapse.
My theory is that the Qunari have concluded that the reason they failed in their previous war is that despite their enemies' lack of real unity, the Chantry allowed/forced them to focus their energies against the greater threat through the Exalted Marches, arguably just like the Crusades in the real world. They had little difficulty picking off kingdoms one at a time, but their numbers were/are too few to win an all-against-one.
In the "Destiny" video, the Qunari's target seems to be the cowering individual with a crown. My guess is he's someone high-up in the Chantry's hierarchy, and I'd nearly think he's the Male Divine of the Tevinter Imperium, but that's probably reading too much into it. Either way their goal must be to destroy the Chantry's structure to pave the way for an all-out invasion.
If I'm right, my guess is the question posed to Hawke by the end of the game is how best to unite Thedas agaisnt the Qunari: must it be through a renewed Chantry, or something very different? I know what my Warden's answer would be ("Hey Alistair dear, can you marry Empress Celene and convince her to push the Chantry to make me new Divine? I know I'm a mage and I don't believe in that silly Maker or anything, but you know I would just love commanding that many fools around, and have you seen the Divine's dress?!") but I don't know what kind of Hawke I want to play yet, so who knows