The Mysterious Benefactor

The first part is off just because the timelines don't agree. TIM wasn't indoctrinated until Mass Effect 3. The Andromeda Initiative took place during Mass Effect 1 and partially during Mass Effect 2. So, he wasn't indoctrinated while making any choices about the Andromeda Initiative. Also, he might have been ultra human, but Mass Effect 2 proved he was willing to use aliens and even artificial intelligence if he deemed it necessary... like it definitely was to get the InitiativeI off the ground. So, none of those points you made rule TIM out of the picture at all.

Having said that, it was obvious that he didn't jump on the arc his self, but he definitely could have planted operatives, such as his daughter Cora Harper who was suddenly and for no reason dropped from the Asari commandos and deliberately pointed to the Andromeda Initiative. What she knows and how she could come into play is obviously still up in the air, but I think her ties will definitely come into play. The new face and new objectives you're mentioning could definitely come from his daughter.

You'll have to elaborate on the third paragraph, because I'm not sure what you're talking about.

Just doing another play through and someone mentioned Calix Corvannis as the instigator of the Revolt on the Nexus and that Sloane changed sides and took up the figure head role. Why do we never here anything else about Calix Corvannis or have I just missed other references?

He died in the revolt.  Sloane didn't necessarily join the exiles because she wanted to.  She just made a bunch of dumb decisions.  At times when she should have been advising Tann she was off doing whatever she wanted and was unreachable, either by choice or accident.  That left Tann, an accountant, to make decisions without her advice.  And even when she was present she was, at best, antagonistic toward the other Nexus leaders.  Going to Corvannis to try to talk him down (it's what she was doing) would have worked out fine if she had just thought for one second to let ANYONE know her plan, be it Tann and Addison or any of her security staff.  Hell, even an email would have worked!  So when security and the krogan were sent against those who revolted, they found Sloane with them.  She didn't even try to let them know what was going on.

To her credit, Sloane was trying to prevent a total bloodbath, so siding with them more or less saved them and allowed for exile (or return to cryo, but they rejected that).  Basically, no one understood that probably no leader could have made things good.  The Nexus was damaged, the seeds for food were mostly irradiated and unuseable, they had very little power on the Nexus and all of the golden worlds were unlivable.  It was a clusterfuck but because of the Scourge.  The problem with the leadership is that they weren't equipped to handle an emergency - that is, in the sense that they didn't have the charisma necessary to soothe people.

Yes, it's from the novel.  Not sure the book gives any more information on the MB.  I could lead you to think Spender killed Jien Garson but if that was done by the MB then Spender was obviously expendable.

I don't know that Sloan's thinking has anything to do with who the MB is. Remember, no one knows the identity of the MB, whether it's one person or many. Also, Cerberus was funded by a great many people, including high ranking Alliance members. They're Cerberus, even if not on the public record as being members. I also doubt Sloane Kelly knows the fully extent of what Cerberus might or might not do. I suspect she'd be surprised to learn that a Cerberus ship had the following as crew/squad: a salarian, a krogan, a drell, a quarian and a turian. Like most, she probably believes they'd never work with aliens, thus thinking they could target the AI.

Now, all that said, I don't think Cerberus is behind anything here. At least, I hope not. It would kind of ruin things. Of all the things that needed to be left behind and destroyed at the end of ME3, Cerberus is right there behind the Reapers.

Btw, TIM was certainly indoctrinated in Mass Effect 2, there's video console in Mass Effect 3 that shows he had reaper tech implanted.

I'm late to the party here having only recently been able to complete the game, but it doesn't make sense to me for it to be Cerberus if only because of the inclusion of all the other races. I like the idea of it being an AI like EDI or even the geth behind it, perhaps?

I honestly wish the murder plotline wasn't included, especially as it was left unresolved. It was kinda dumb, and I'd have liked to see Jien Garson in the game.

I'm seeing something similar.  The original Shadow Broker setting this up, funding it, having it set up so Reyes could take out Jien after landing, and setting up bumbling Credits-Jugglar as his/her face running the show.  Even in the book it was a huge surprise to everyone that they put the accountant the succession of who would be in charge in case of catastrophe ahead of Addison and Sloane.  Something got switched there behind the scenes and if Jien had caught it, well there's that reason to take her out.  Shadow Broker wanted his/her own person as a figure head, not someone that would give him trouble.

I'm not sure who Ryder could tell.

Anyone awake at the time of the murder is a potential suspect.  SAM says the murderer is probably long gone, but there's no proof of that.

the benefactor is Miranda's dad.
And he got TIM to pitch in.
He was probably planning on Miranda to join but she was stuck on some zombie project which took two years. She missed her flight to Andromeda.

Well, it's apparently "easy" to break out of your own stasis pod, because Avitus Rix managed to do so with his pod. Yea, Kandros doesn't sound like a guy that could commit murder/conspiracy. 

Reyes Vidal. He's already shown himself to be a lying, manipulative murderer, with access to lots of resources. We know very little about his background. We do know that he was on the Nexus when Garson was murdered. We've also seen that he likes to remain in the shadows and let others be his public figureheads. Plus the writers go out of their way to make sure he survives this game. Even if you try to shoot him, he gets away.

They already revealed him to be The Charlatan. No one would suspect a second reveal of him also being The Benefactor.

There have been some good theories in this thread that actually I agree with. I'm just throwing this one out there as another possibility.