Of the three listed, I would say the Geth are the most likely. The only thing I have to wonder about is, it SEEMS that Jien Garson was killed by the Benefactor forces.....which doesn't make much sense if it was the Geth. She would have made a huge difference in survival of the Initiative due to the ability to get people to continue to work together. But other than that, yeah, there are many reason to think the Geth are the Benefactor.
Yeppers! The Jien Garson thing is sort of messed up, Tann originally say's she was Scourg killed while still in her stasis pod, but then latter in the story she is killed by some unknown attacker.
I never could make much sense out of that whole deal.
It could be that she was not nearly the asset to the Initiative that everyone seems to think, she may have even been a problem, as she could have revealed the benefactor, and may have been trying to do so, and was silenced for this reason ( She was wanting to talk with Alex as soon as she could about problems with the benefactor ). The Geth would not have wanted anyone to know they were the benefactor, so that speculatively could have been the reason for her Murder, and the hiring of a Hit person or assassin, would not have been that hard to purchase from any of the perspective benefactor's.
If a Geth Intelligence was onboard the arc ( or if it was part of Sam ), it would not have needed to be in Cryo, so they could oversee all situation's as they occurred. Also If Sam was a part of it, connected with the Geth, many parts of Sam's Memory are blocked, Sam might not even be aware of some thing's that they were programed to do or that sub system's in there programing might automatically do.
You would think Sam's overall understanding of all thing's would have been better in regards to the funding, yet he is almost like a Blank space when ever asked about the benefactor, offering truly very little to help uncover them. ( The Crime scene of Jien Garson being really the only helpful injection that Sam Made ).
I thought the Illusive Man was the primary suspect, and killing Garson is right up his alley. However there are things that don't line up, namely funding other species arks, which goes directly against Cerberus's ideals. The Geth are possible, but they were largely reclusive regardless of faction so I don't see them really doing it, especially since the other races were so distrusting of them.
Shadow Broker is a distinct possibility after Liara took the mantle and she did have a cameo in ME:A.
I'm not sure the trilogy really provides any other entity that would have the resources and agenda to really push for the Initiative though.
I tend to think of the general Shadow Broker succession operates like the Dread Pirate Roberts succession, where the current guy stockpiles his loot, and, when he wants to get out, cuts out the key bits of info he doesn't want anyone finding out from anywhere, and leaves his apprentice with the rest. Personally, I think the Benefactor is the Shadow Broker before the Yahg, and, having discovered that the Reapers are coming and has decided to take his retirement in another galaxy.
TIM is another good option, especially if he wrote of the MW for now, left a clone in his place, and went to ensue human dominance in Andromeda. There are little things, such as the tablet with sensor logs in the prologue and Tann, which make me think that the Initiative was intentionally sabotaged even before it arrived and hit the Scourge and Kett. Certainly by the end of ME:A humans are in a dominant position among the MW colonists.
There are a bunch of other Benefactor ideas and discussion in other threads if you check out the links in the Collected Ideas and Suggestions at the top of the page
