Technically, Face takes over fairly early in Solo Command. He's promoted to brevet captain (essentially a trial run) and Wedge goes back to leading the Rogues (while also serving as overall CO of Mon Remonda's four squadrons), and the captaincy is made permanent at the end of the book as Wraith Squadron gets de- and re-commissioned away from Starfighter Command and over to New Republic Intelligence. Face continued to lead the squadron up through Darth Caedus's rise, but Daala disbanded them when she took over the GA. After the events of the Fate of the Jedi series, Face was tasked to look into corruption in the GA and reactivated the Wraiths unofficially.
http://starwars.wikia.com/wiki/Wraith_Squadron has more, but since I've got a Wraith Squadron-inspired tattoo, I damn well better know their story.