Enhanced wrote...
*Pyramid Prevention Snip*
You're right, it wasn't implied in any interactions with the Reaper themselves. But, at the end of ME2, we learn that every Reaper is a collective intelligence of organics minds. It didn't make sense that they would all just turn against evil and start killing/harvesting other races on their own. I assumed that Harbinger was controlling them .The ending of ME3 is supposed to be the plot twist. And, the Control option proves that they are all forced.
Well, actually we don't learn they are a collective intelligence. To my recollection all we learn is that the Reapers are quite literally melting people down and dumping them into a Reaper shell. It's less a twist and more horrific reveal, "Soylent Green is people", here is the terrible truth: we organics are nothing but raw materials for Reaperduction. In fact to the best of my memory the only thing that infers the minds are still there is in Legion's extremely obscure and hard to obtain dialogue that I think I have seen a grand total of zero times in my many playthroughs of ME2. Even then he says nothing as to the state of the minds, or what remains of those killed to make the Reaper. Certainly the process of creation doesn't give much reason to assume anything is left of them.
Comparing this to what we have seen of Reaper constructs to that point I don't see why we should expect anything to remain, husks certainly seem rather mindless, cyber zombies in fact. And Mordin explains quite clearly that there is nothing left of the Protheans should Shepard express a desire to help the Collectors.
Further character interaction is an essential part of forming opinions in Mass Effect. The only reason I think better of the Geth is from meeting Legion. Prior to that point all Geth = Bad Guys, but then we meet Legion and not only does he save us, he proceeds to talk to us, somthing no Geth has ever done. Then when we get back to the ship, from talking to him we learn there is more to the Geth than we have been led to believe. And had we never met Wrex, or Grunt, or any of the more friendly Krogan, or done Mordins mission, if all we saw was the brutal savage and blood thirsty ones who tried to kill us, my opinion of them and curing the Genophage would be remarkably different.
In our interactions with Saren, Benezia, Shiala, TIM, or anyone under Reaper thrall we can in some cases detect them resisting Reaper control, we can break through and see that they are not yet completely lost, but of the Reapers there is nothing but cold indifference, disgust, and contempt for those beneath them.
So how we have interacted with the Reapers, and how they interacted with us is I think absolutely important for us knowing what they are.
The "plot twist" in the final minutes of a three game trilogy is I think a huge problem too. If it is indeed trying to say the Reapers were toothless and all rainbows and daisies, it completely clashes with everything seen prior. It would be exactly like Sauron turning out to be a good guy just as Frodo reaches Mount Doom.
And I'm not really how Control proves anything as far as Reapers being forced. Pre-EC there was nothing, and post-EC they are clearly being controlled or "forced" by Shepard to rebuild the Relays and obey his/her/it's will, but them being forced to obey Shepard 2.0 does not prove they were being forced to obey before. It doesn't really tell us anything, anymore than Frodo becoming the Lord of the Rings and forcing the Nazgul to work in a soup kitchen proves they weren't evil before.
Also somewhat related to this discussion is this quote from Mac Walters in an article posted January 27, 2012:
"You can't go and find one Reaper who actually turns out to be a good guy… things like, "Oh, yeah, these Reapers are OK." People playing the game will hopefull say, ‘Nope. They're as bad as everyone said they are.' You really don't want to be doing anything but killing them."
Source: kotaku.com/5880034/how-bioware-writes-a-mass-effect-game
Granted, given the track record of pre-release quotes that's probably worth about as much as the pixels it's printed on.