As we know, Legion's loyalty mission is basically about uniting the Geth under one banner (or directive). Regardless of your choice at the end, the rebel faction that was led by Saren was ended and Legion asserts that all Geth now share the same ideal.
Now I just realised that one of the screenshots I've seen is that of Shepard using his new Omni-stab against a Geth Trooper. Now until now, I'd believed that the Geth would be one of the ally races that you'd recruit into your Grand Army of the Citadel! I suppose there are any number of theories as to why there would be Geth opposing Shepard in ME3; what are your thoughts on the role of Legion and the Geth in Mass Effect ?
Personally, I'm totally confused. My guess is either Shep and Legion didn't manage to wipe out ALL the Reaper-worshipping Geth, or between ME2-3, they've had another clash of ideas and a faction of Geth has split from the main nexus.