The last encrypted message from Alec.[Spoilers]

TIM had been indoctrinated long before Mass Effect 1, There is a comic that cover that and It seems that his eyes are from that (He touched a Reaper device as Saren and his related turian that died in that comic)

Biggest reason, I don't think it's Cerberus, or TIM, is they would only fund Human Arks, and wouldn't have sought Council approval.

I think it was the original Shadow Broker, and the reason he was confident he could evade the reapers, it also explains how Liara knew of the Arks existance.
His plans went south when Liara replaced him. it also explains why things went bad, as his agents were left to fight for control.
Two fanctions emerged, and both the current leadership of AI, and the rebellion have want to be "Shadow Broker's", pulling strings from the shadows.

Maybe even more than 2 factions exist, but until Ryder arrived to follow the public AI goals, the SB's aims were focused on destroying each other.

Tann's Shadow going for the Control Nexus approach, and Exile's Shadow using the Isolate Nexus, and Starve them out.
The entire plot is so full of holes, like why was the Scourge not seen on approach, even if you accept the Nexus missed it.
It would have QEC links to each Ark, yet no warning was given.

Then there's the size of the Nexus It's massive, and the events after arrival mean it remains in the umfinished state it arrived in, with added damage from the scourge.
Why were Arks even needed, all the colonists could have been on the Nexus, Redundancy, and polotics, I assume.

Then there's the giving up on Arks after only 14 months, when the Nexus was intended to arrive first, and be fully constructed by the time they arrived.
How long was that construction supposed to take, from the moment I arrived, I considered the Leadership of every faction to be incompetant, if not actively working against the public plan.

Don't get me wrong, I enjoyed the game, more than all the others, but I never have understood the idea that Bioware are goood at story telling, the previous games had just as many major flaws, in the plot, huge holes that made no sense,
They are reasonably competent, at relationships, but rubbish at the big story details, and consistancy, and were with the trilogy.