Ellie will probably become the new Intersect. With Chuck as a fully fledged spy he doesn't really need it any more to remain on the team. Actually, they are hardly ever using the Intersect thing these days in most of the stories anyway. Having Ellie flash (fnar fnar) would be a good way to change the dynamic a bit while keeping all the players in the game. I'm waiting for a parallel to emerge between Ellie and their mum if Ellie takes the road to superspy, just as they did with Chuck and their dad.
I agree on Dalton's turn being obvious but it was fun waiting for it.
"Oh cool! A tiny weapons stand-off" had me totally cracked up.