SPOILERS >The benefactor of The Andromeda Initiative?

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

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.

Personally, I don't think the Geth are the Benefactor for the same reason you think TIM isn't: the other races. The Geth may have wanted to keep the Quarians, one of the smaller groups in the Initiative & a possible failure to launch, alive, but they had no reason to send the others, especially as no one but a few renegade humans were trying to support AI.

As for TIM, the Benefactor just made the project feasible. before launch every major shady outfit in the galaxy had gotten involved, undoubtedly ensuring the participation of their races in this venture. Nevertheless, the human ark was the only Initiative vessel to survive a Scourge crash (and a planetary crash landing) with minimal damage and few, if any, fatalities. In addition, due to circumstances not entirely out of the Benefactor's control, humanity has total control over the most powerful alien artifact in Helios and dominates the Initiative's outposts, while the Turians and Asari have lost large portions of their populations and the Salariens have been slaughtered so much that their racial sustainability is in question.

Still, you present some good points. I would love to see your views on some of the other alternatives that people have suggested for the Benefactor.