Imo, the only big loose thread left in my eyes is whatever the frakk was up with Lady M and Xaos, which probably won't be touched for the foreseeable future thanks to HG. With regards to the other shady organizations; everyone involved in the Vajra incident is paste on the walls of a ship that probably isn't even in the galaxy atm, Vindrance was the military equivalent of five dudes in a souped up van who blew up in Zettai Live, and the Epsilon Foundation is basically just Anaheim electronics from Gundam. For better or for worse, there's not a lot left to grapple with in a new show, barring a straight up sequel to Frontier, and even that isn't really tying up a loose end so much as emotional closure