1. I personally totally don't feel that TIM is the one to look at, mainly because to much money spent on other race's.. Just is not his MO.
2. The Geth were not truly elusive ( they had tried to stay in area's away from Organics, The Old machines were the reason for the Geth Heretics return ), they had become a split ( until Shepard United them, or re programed the Heretic's or killed them ) , some believing in the Old machines as there God, and the other half, denying that, and trying to find a way to fix the relationship with the Quarian's, and also perhaps to save themselves from the Old machine's ( transferring there consensus to the sam's of every initiative ship would have been a sure fire way to escape the old machine's ).
They would have known that the Old machines were coming for sure. They also knew the Old machines did not like them, and looked down on them. This would have been a very good reason for them to ally with the other races, but of course would have had to do so in secret.
Knowing that and AI would be symbiotically united with an organic, would have been a harmony they would have been very happy with. Existing as equal's.
EDIT >> The killing of Garson would make perfect sense, as she was trying to expose who the benefactor was, and if they were found to be involved, all out riot, would have been been the result from the Organic's, and The Sam unit's would have been destroyed along with the entire pathfinder Initiative. <<<End Of Edit
( This also falls into line with much of what it has seemed, that Bioware has been trying to push, in the Green colored ending of ME3, The writers seem to be hung up on this cybernetic merging of Man, and Machine. )
Sam has a personality that is very much like Legion's personality, for me the Geth make the most sense Alex even seemed to based Much of his research from the Quarian's Geth creation.
3. The shadow broker could fit in nicely, in some ways with the time line, as when Liara takes over we are led to believe the creature she took over was there Killer, but what if they were not dead, but in a Cryo pod headed for Andromeda, and had given what was left of there information gathering service to the Creatures control, who appeared to be in charge.
I do not totally rule out the Shadow broker, but I still see the Geth AI intelligence as a better choice, and more logical or sensible to me anyway.