I thought the Illusive Man seemed rather villanous in Mass Effect 2 especially considering the experiments Cerberus were running and considering how I believe EDI states that the Illusive Man only keeps as many cells as he personally can keep track of so I question the idea that he was entirely unaware of what some cells were up to.
Regardless of whether or not the experiments escalated from their intended purposes without his knowledge, the beginning of the experiments Cerberus conducted were villanous such as faking the death of children so that they could be abducted for experiments with the parents of said children none the wiser.
The Illusive Man may claim well-meaning motives but I would not consider him nor his methods to be ambigous.
- Bringing Shepard back exactly as he was. There were a million ways he could have altered Shepard (and, as we find out in ME3, Miranda wanted to implant safeguards). It was clear from the events of ME1 just what kind person Shepard was. Eschewing safeguards is not the action of someone with villainous intent. Obviously a plot-device, because if there had been a control chip, TIM could have just flipped a switch and voila, Shepard does what he's told, end of saga. But it is what it is.
- Even after previous brushes with Cerberus in ME1, saving the colonists in ME2 from the Collectors seems an entirely altruistic endeavor. Depending on how you decide to play Shepard, it can seem this way all the way to the end of the game. It can even be argued that it remains that way through the end; the idea of salvaging the Collector base wasn't something TIM planned on (since he didn't know what the base would contain), and his arguments about analyzing how the Collectors were building a Reaper ring true - someone might hide the guilt over the lives lost and take the intel (Vega makes a similar ethical decision in Paragon Lost). Though this depends on how you play Shepard.
- TIM enlisting aliens to help with the Collector problem seems to indicate that not all the xenophobia of Charles Serracino (a Cerberus-backed political candidate from ME1) was true. Conversations with Kelly Chambers further point to Cerberus not "hating" aliens. So TIM can't be that bad, right? It isn't until ME3 that we learn that the entire Normandy SR2 crew was selected to confuse Shepard about where his /her loyalties lay.
- If told about the derelict Reaper trap, I believe Shepard absolutely would have "tipped off the Collectors in any number of ways." Secrecy and stealth are not Shepard's forte (the Normandy's, sure, but once Shepard is on-site, it's never long until the shooting starts - excepting Arrival, and even then the guns come out once Kenson is rescued). Jacob and Miranda were good soldiers, but Shepard was N7. Once the shooting started - and TIM knew it would - he had to have his best operative in there.
- Project Overlord can be explained away as TIM trusting Gavin Archer to get the job done without interfering - and TIM is usually hands-off for individual operations; Shepard (after he was resurrected) and Grayson represented exceptions. TIM set the bar of his expectations high, and Archer would rather torture his brother than fail to meet it. But there is no indication that TIM knew what David Archer was going through as he was going through it. After reading the Mass Effect novels (Ascension and Retribution) and playing ME3 I have no doubt that he knew.
I believe EDI states that the Illusive Man only keeps as many cells as he personally can keep track of so I question the idea that he was entirely unaware of what some cells were up to.
I don't recall EDI saying that, though I do remember asking her questions about TIM. I could be wrong, obviously. Her "core programming" prevented her from answering. Maybe if talking to her after the Collector abduction?...
- What happened on Pragia was without TIM's knowledge, as evidenced by the video logs found at the facility. There is no evidence that the Pragia research base was ever established as anything other than a biotic research facility. Whether he even knew about the abductions of children is uncertain in ME2. Again, after reading the novels and playing ME3, I have no doubt that TIM knew about the abductions - and would have approved of Pragia's efforts once he found out. Though it's interesting that the operators of the facility didn't think he would.
TL;DR There were a lot of things in ME2 the very first time I played the game that had me wondering about the true nature of TIM - ergo, ambiguous. Since different conversation choices could emphasize or de-emphasize certain things, I was even more confused the second time I played ME2. Played ME3, read the novels and comics, and it's pretty clear imo what type of character he is, where he's coming from, and what he knew.
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