I hadn't realised the idea was contested and a quick skim of the wikipedia entry you linked doesn't seem to suggest that either but, I'm no expert on the subject!
Ah, that was my fault. Not only did I link wikipedia, I also linked the wrong article, sorry. Here is the one I wanted.
I haven't read the whole thread (sorry) so I'm curious why the suggestion that the Reaper's aims were driven by the application of cold logic towards the goal they believe they were created to achieve diminishes the ending?
While I do think the Reapers are shackled, given that the Catalyst says that it controls them, i don't see why its goals or reasoning would imply that it must also be shackled. Just because an AI is sentient and free to choose doesn't mean it wouldn't want to choose to perform the purpose it was created for. Edi asked for her purpose and, essentially, Shepard set it for her so I see no real difference there.
Ah, if you are curious, please do read the thread (it's not that long yet). But this was my post on the VI/shackled AI issue. In short, I just find it unsatisfactory that we'd fight a program that was created on an idea that the programmer (read: Leviathans) never really thought through.
That wasn't directed at you specifically, just the idea. What pointless nitpicks weaken the criticism? He does indeed nitpick some places but that doesn't mean he puts too much weight on them, but merely mentions them.
It's just, every time I watch his videos, I cringe a lot and think "Wow, this could be explained so easily" (I said the same in my first post here). Unfortunately, I can't watch the video right now and I can't remember specifics but it happens a lot. Maybe I can edit this post later today, when I am home and can try and find an example.
As Tim van Beek said (I think in the other thread, it very much depends on your definition of what is considered a plot hole. His is just so much wider than mine that we don't see eye to eye on a lot of issues. I suspect that you have a different perspective on it though. 
Again, the Catalyst's premise isn't that they might, it's that they will. But the Geth would have been eliminated without Reaper intervention.
But the catalysts point is not that the Geth specifically will be the AI that destroys organics, just that there will be one AI at some point that will do it. And if you presume that he can wait infinitely long, I suppose there is no way to disprove him because "might" and "will" are equivalent.
The premise is of course meaningless because you could just as well use any other reason instead of AIs but you will not be able to disprove the hypothesis.