If by "hate", you mean "favorite character to hate", then I would say the Illusive Man (TIM).
Partially because I find myself agreeing with him on a few things (The Council takes too long to act, Humanity needs to be self-sufficient, Humanity needs an answer to the various threats the galaxy throws at us, etc.) but the methods he uses are where that agreement ends.
I agree with the initial idea behind Cerberus. There is a lot of scary crap out there that wants to kill us, or eat us, or both; so having a guardian of the Charon Relay (nice mythological bonus there) is something I can get behind.
Also, the Salarian Special Tasks Group (green), Asari commandos (purple), Turian Cabals (orange), and Krogan shock troops (red); they're the "face" of each races' military forces and go-to strategy.
So I agree that the Alliance (blue) needs a response to that, hence Cerberus (gold).
I like how, at least in ME2, you were the only group doing something about the Collectors. While bureaucracy bogged down the Council and the Alliance, you were able to get in there and GET THINGS DONE.
As Miranda says: "We have an assignment, we can talk about it, or we can do it."
In addition, without Cerberus, the Normandy might never have been conceived. We all know how pivotal that ship and her captain were in the Reaper War.
Their weapons I find to be among the best in the game, rivaled only by the N7 weapons. Of course, how do we know that Cerberus didn't have a hand in those as well?
That said, the deceptive experiments (think: Overlord and Sanctuary) are too far. I didn't feel bad about using the information gained from those abhorrent events, (except I'm NOT leaving David Archer, I'm freeing him whether you like it or not) because it's my way of making it so that there's at least a benefit to what was committed.
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Some of my favorite non-combat parts of Mass Effect are when you are talking to TIM, and trying to persuade him (Paragon) to help you instead of trying to control the Reapers, Shepard's responses in that regard are very much like something I would say:
"Work with me then, give me control of your resources, and I'll stop them."
"You're doing exactly what the Reapers want!"
"You're indoctrinated, can't you see that?"
"Then do it! End this, right now! ... They won't let you, will they?"
"It's not too late, we can stop this."
Heck, even some (Renegade) options sound like me:
"If you don't, every man, woman, and child is dead because of you."
"You're nothing more than the Reaper's puppet now."
"Humanity counted on you, and you failed them."
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Regarding the Illusive Man himself, he is extremely intelligent (so am I), and is very persuasive (so am I).
The difference being that I don't manipulate people, so that's another "broken mirror" reflection.
I see the Illusive Man, and it's like looking at myself, if I were to become a villain.
That's part of why I like the ultimate (Paragon) persuasion at the very end...
Being able to convince the Illusive Man that he's indoctrinated and that he can fight it off, followed by the scene where he says "I'm sorry, Shepard, I tried..." *headshot*
That, for me, is a poignant moment. You see that TIM as you've dealt with him prior wasn't fully him, so it's like meeting someone for the first time, only to see them cut down in an instant. It makes me wonder what he would have done if he hadn't been indoctrinated, but it's also liberating, to see that "right makes might" and that TIM was finally freed from Reaper influence.
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All together, I admire the Illusive Man's commitment, drive, and foresight, even as I despise his ruthlessness, his unwillingness to compromise, and superiority complex.
I "love to hate" this guy because I see so much of myself in him, but I also see how we are VERY different, so in a way it's like I'm talking with a different version of myself. It makes for excellent role-playing and if nothing else, I freakin' LOVE the Eviscerator.
Seriously, armor-piercing (High Velocity Barrel), long-range (Smart Choke), flamethrower (Incendiary Ammo), explosive (also Incendiary Ammo) shotgun!
Oh, what would I do without that shotgun? (most likely switch my Phalanx with the Talon, that's what, and then carry the Hurricane instead of a shotgun, but that's not the point!)
That, and TIM's office is something I would love to have for myself.
Good idea (at first), exceptional equipment, and nifty color scheme, it's almost perfect, except for the "EVIL" part.
The Illusive Man is the character I "hate" the most.