The Benefactor is...

...Commander Shepard.

Think about it. Shepard knew about the reapers, and there's the gap between the end of ME1 and the start of ME2, where all the credits and stuff you mined just disappeared. Where did it go? It funded the Initiative. How did Shepard know about the initiative? They went to the moon in ME1, where we saw the arks being built in the trailer.
But why would Shepard fund the AI instead of fighting the reapers? Because they knew they couldn't win. So Shepard planned to go to Andromeda, so that the Milky Way species would eventually return, to defeat the reapers while they hibernated in darkspace.

Of course, Shepard died and missed the departure date. Or did they? 

Shepard faked their own death, and actually escaped from the SR-1 with Joker before going into hiding, preparing for the arks' departure. Meanwhile, a fake Shepard corpse was left for Cerberus to find and execute project "Lazarus" on. The Shepard we used in ME2-3 was the fake Shepard, used to distract from the real Shepard's actions as the benefactor and to keep Cerberus from infiltrating the AI. However, fake Shepard found out the truth, and planned to reveal it to the council, so was disposed of by Shepard's allies who remained in the Milky Way and replaced by a second Shepard clone.

The crucible was just a plot to keep new fake Shepard busy and distract the inhabitants of the Milky Way from their impending doom, and the catalyst was a figment of fake Shepard's imagination to ensure fake Shepard would commit suicide before they had the chance to discover the truth. The clone Shepard you fight in the citadel dlc is in fact the first fake Shepard, who survived the attempt on their life and planned to reassume their original identity to reveal the deception.

Meanwhile, the real Shepard travelled to Andromeda, killing Jien Garson when she threatened to expose the truth and reveal that everyone in the Milky Way was dead. Shepard is now overseeing the Initiative, acting through Director Tann, to prepare for the return to the Milky Way where Shepard's allies from ME1 are waiting, have entered cryostasis just after fake Shepard died.

What was not anticipated, though, was that the quarian ark would be delayed long enough to discover the truth before it left for Andromeda. Hence, knowing that Commander Shepard would attempt to arrange an "accident" to destroy them, the ark sent out a message to the Initiative warning them to keep away to buy them time. An upcoming DLC where the Tempest goes to rescue the quarians will see Ryder fight against, and defeat, the real Shepard (the reason the game asks you to input Shepard's gender), before choosing whether to reveal the truth to the entire Initiative or continue with Shepard's plan to destroy the reapers.

ME3 endings circumvented, Shepard returns, all is well with Mass Effect once more. Bioware can thank me later.

tl;dr ME2-3 aren't real and Shepard fights Ryder on the quarian ark.