ExoGeni-Cerberus Link?

If one asks EDI questions about Cerberus Resources and then "billions" in ME2 after Joker unshackles her, she does indicate that Cerberus uses several legitimate businesses as "fronts" and several wealthy contributors within the Alliance military complex. I don't believe it is ever explicitly stated, but I think it likely that there is some sort of connection and almost every corporation mentioned in the game. In the Codex under Cerberus: the Illusive Man, Cerberus is described as an "untraceable syndicate of private intelligence agencies, biotics laboratories, engineering and scientific research teams, and lucrative front companies."

ExoGeni has no redeeming qualities? That's a bit harsh. Exogeni has done a lot of unethical experiments that Shepard has found, but there are other, less evil Exogeni projects. For example, terraforming Trebin by introducing more water into the atmosphere.

Anyway, on topic, I think Cerberus must have a pretty strong connection, as they must have got the Thorian Creepers from somewhere. If you keep ME1's lore alone, Cerberus are an Alliance cell, and Exogeni work quite close with the Alliance according to Udina.

And with ME2's Cerberus ret-con, it's said that the Illusive Man has shares in all sorts of companies, and as Exogeni is a big company, one would assume they work together.

Cerberus might work with them under assumed names but direct link I doubt it.

No long part of the Alliance - true.  However, EDI's statements in ME2 indicate that they still get financial support from some whigs in the Alliance.

Absolutely agree... but it's not hard to head canon a larger conspiracy if you want since it reveals that there is a portion of the Alliance brass that is sympathetic to Cerberus ideals.  As I said, it's a story line that really wasn't developed beyond those few little hints in ME2... so players can ignore it completely or take it to whatever depths they want.

ExoGeni does good work.

Cerberus agents were found in ME1 with both thorian creepers and rachni. In one case, both on the same planet where you find Admiral Kahoku's body. ExoGeni was studying the effects of organic-based mindcontrol. I think that would have been an interest of TIM's even before ME2. If ExoGeni was a Cerberus front, it would explain how their scientists got ahold of thorian creepers.

Not only do I think that ExoGeni is one of Cerberus' legitmate fronts, I think the same of Binary Helix. Helix has even got the colors going on the Peak 15 tram and on the image that stray posted. White tram, black trim, yellow number. Explains how Cerberus was able to track down or recreate the Rachni queen.

I think pretty much the same thing.  The kicker, though, is that indoctrinated Saren was a major player in Binary Helix.  As was indoctrinated Matriarch Benezia.  To me, that suggests that TIM may have been at least partially indoctrinated as early as 2183.

The funny part is, Mass Effect 2 would have been the perfect chance to tie up the loose ends with ExoGeni and Binary Helix. Just imagine doing quest chains involving each company hiring the Blue Suns or Eclipse mercenaries, and Shepard takes their operations down one by one for either Cerberus or the Alliance. 

True that. However, it doesn't change how I feel regarding TIM being possibly indoctrinated that early on. He's been shown to use aliens to his own gain before. My guess is that TIM was already involved with at least one corporation (probably several,) and when Saren showed interested in the company, TIM took advantage of it.

I do think that the cloning was done on the downlow. TIM has a lot of contacts and resources, but that doesn't mean he knew everything that happened. I'm also guessing that Saren showed interest in the rachni because he was interested in studying how a hive mind can work. That and probably Sovvy put it into his head that, if they were rendered mindless, rachni would make an excellent weapon for terror. Fear can make willpower break down that much faster, which means that the subject would become easier to control.

The real question I've always wondered about was how long Saren had been indoctrinated prior to Eden Prime.

I'm going to add some speculation here about the nature of a link between Cerberus and the Alliance. EDI tells us in ME2 that Cerberus contributors include whigs in the Alliance military complex. I'm just doing the Corporal Toombs mission on Ontarom, where Toombs reveals that Cerberus used him as a "thresher maw" test subject. When Hackett informs Shepard... he describes the "former Alliance scientists" who are being killed only as having worked on "a classified project on Akuze." It would be more natural for Hackett to use this sort of phrasing if he were describing a classified project within the Alliance... not a rogue project being run by a disavowed black ops organization. Just food for thought. Did the Alliance order/sponsor testing like this on their own troops?