Spoiler Enter if you've completed the Ryder family memory quest.

Why do I get an itch that Cerberus is a part of this.

that big ass remnant is thresher maw 2.0 HEHEHEHEHE

and cora is secretly a cerberus sleeper agent who we screwed also.  Decent rack like Miranda who they originally drafted as blonde.

Where did you get that notion?  I don't recall, personally.  Putting in hours on this game makes it tough to catch every detail.  From my recollection, it seemed like Jien got cold feet prior to leaving the Milky Way, sent a message to a newly cryo-sleeping Alec before she, too, went to sleep, and Alec got her message after he awoke in Andromeda.  Jien got murdered in Andromeda.  But didn't the Benefactor's communications/messages only play in and originate from the Milky Way, not Andromeda?  

If Cerberus is at large again, and signs point to yes as it was humanity that got the boost and humanity that needed to continue even if the Milky Way's humanity died, then chances are good that TIM was directly involved, especially considering his paranoia in ME 2.  If TIM isn't the Benefactor, then it could be an underling or a new character akin to a human Shadow Broker.  On a meta level, it could be that Bioware has yet to secure Martin Sheen's voice again.  But to me, Benefactor implies $$$, so that's all TIM, supremely wealthy.  Then there's the Cora connection, so...  

Anyway, it excited me to think that Alec has so much in common with Anakin/Darth Vader (e.g., twin son/daughter, sacrificing a noble career, turning to the forbidden, trying to save a dying wife) that I was really hoping (c'mon, Bioware, this is in your wheelhouse!) that TIM was going to be revealed as Emperor Palpatine/Darth Sidious.  Ha ha.

I just finished all the videos.

Now that was some good story writing.

Andromeda has potential. I imagine the next game will be better. ME2 2.0 if you will

In the prequel novel, Nexus Uprising, Jien is awakened and alive when they reach Andromeda, and disappears shortly after the collision with the Scourge. Not to mention her corpse was too fresh to be 600 years old or frozen when they found it. She was not killed in the Milky Way, so unless TIM cloned himself or can be in two places at once, he's not the murderer.

Cerberus scientific experiments are fascinating.

It's like digging into the Nazis work--neither are limited by morality

TIM doesn't do anything himself save for confronting Shepard in the Citadel Tower, everything is done by agents.  Giarsen was killed by one of his agents.

There were eerie similarities between ME1/ME Infiltrator Cerberus and the Kett.  Different agendas, but similar actions of study/dissection.

Doesnt compute, TIM wouldnt fund arks for all the other races but just send a human ark out.

Also, the Benefactor seems to know or at the very least suspect about the Reapers before Shepard becomes aware of them and any evidence is uncovered.

My money is on the Shadow Broker.

He/she knew about the Reapers. Has the network to build the cruicible (well Liara did, after taking over), which is comparable in scale and perhaps even more technologically challenging. The Yagh we fought in Lair of the Shadow Broker is stated to be a pet captured by the former Shadow Broker according to Liara. Liara thinks that the Yagh killed the previous Shadow Broker. I think she's wrong. I think the Yagh was given the network on purpose and it was made to look like the previous Shadow Broker was killed by that Yagh. That way the Shadow Broker can carry on with his or her shady business in a new galaxy without being bwwrrrrt'ed by the Reapers.

There is absolutely no way it is the Illusive Man. He was indoctrinated and died in Mass Effect 3. I cannot find any way he could have made it to Andromeda, especially since he was in the Milky Way AFTER that the Arks left for Andromeda.