I'm very sure we killed all other Awakened Darkspawn...unless something else is awakening them
There's a possibility of letting The Messenger go. The slides at the end say he travels around and isolated outbreaks of the taint occur in corresponding locations.
The Architect didn't seem to know where he came from or why he was sapient. Some people suspect he's another magister, but it's unclear what the deal was with him. It's possible that other magisters could have already been active besides Corypheus, or that others were created in the same method the The Architect was, if he's not a magister. Either that, or there were just more intelligent darkspawn than we realized.
When I first played Legacy I got a glitch that was popular early on where they said The Architect was spared when that wasn't actually my choice, so I don't know what Nathaniel says if he was killed. To be honest, I would have spared him, though, if I realized the extent of the plot at the time. It's likely the choice I'll make in the keep.