I reloaded some old saves today to try finish building 'relations' with Legion; He says some interesting things in the final two chats.
Spoiler Alert, click show to read: 

First thing worth noticing was that he says the Geth maintain the Quarian home-world as a sort of monument for all the Quarians who died there. Next time he says the Geth are planning to build something akin to a Dyson Sphere into which they'll all finally upload.
Both seem quite harmless, and I'll wager that if the proper Paragon choices are made, in ME3, we might most likely see the Quarians and Geth make peace and co-exist peacefully. Now if the player's choices can affect something of this magnitude, in ME3, then that will be awesome.