After watching the finale, I wholeheartedly hope Jon Favreau takes over all of Star Wars. They did a phenomenal job with this smaller scale episodic series. The Scout Trooper scene just screamed that Favreau gets "it."
it's been reported that Favreau, Filoni and Michelle Rejwan will be the heads of Star Wars going forward (essentially they all replace Kathleen Kennedy)
more than likely they will over see tv series, animation and movies, respectively - but with a lot of interaction and interdependence