According to the lore, there are very few major enemies alive in Destiny

If we consider the races, well.. -Hive: after Crota's and Oryx' Fall, they are completely destroyed. -Vex: we purified the Black Garden, killed Atheon and destroyed almost all Axis mind in the Solar system.. what else? -Cabal: actually there isn't so much lore about them, but they were only running away from Oryx, and we killed all their Majors and Oryx himself. I like to believe that we cancelled only a legion of a legion of all the Cabal Empire -Fallen: well.. we actually killed all the Kells, Archons and Barons in the System. Only one (always according to the lore) is still alive: Kell of Kings. So.. i think the next update will bring him with a whole bunch of Fallen.. or maybe a greater version of a Cabal legion.

(If you have seen other possible enemies please reply)