Barbara taking control was my favorite part of the episode. She was the last one standing in the melee. She improvised and gave orders to Nightwing, which he followed without discussion or argument. She ran Alpha Squad for what might be the first mission against this enemy that ended just as planned - everyone got away and nothing blew up.
She saved them all with her quick thinking when the bioship was flooding, too. Nightwing was preoccupied with how Artemis and Kaldur made out, M’gann was useless, Superboy was KOed, correct me if I’m wrong, but that makes Babs senior officer on the ship.
To everyone who is worried that Stephanie Brown’s appearance means The Killing Joke is definitely in YJ Babs’ future, consider this: Steph was being kidnapped by the Reach, which means she either has the metagene or the potential for it. This Steph is already different from comics!Steph who had no superpowers, just like the rest of the Batfam. Also, she doesn’t go straight to being Batgirl anyway - she was Spoiler for a lot longer, in fact. Spoiler is the identity most of her fans expect she’ll get back if DC re-introduces her to the New 52 at any point.
AND we already have evidence that Young Justice is totally willing to take a comic character and change them a lot to suit this story: Artemis. Stephanie could end up being Stargirl (she was captured in Star City, after all) or Terra, or Liberty Belle, or any number of lesser-known superheroines with blonde hair.