Shepard and Co. failed. Who leads the next cycle in 50,000 years? My vote is on Yahg, Thresher Maws, and Rachni as the new Council.
The Reapers left the Yahg alone, Rachni seem smart enough to evade notice and go into "hiding" as even Javik thought they were extinct. And as for Thresher Maws... well, as Javik said, the lizard people used to eat flies and lick their eyes, so a bug that can think isn't out of the realm of possibility!