I'd say the first really big scratches appeared at the DCS mission in ME2: "They are going to attack earth" or something similar 
Second notable mention to Harbys trashtalk, but the rest-awesome of the game held it pretty much together.
As for the ME3 Catalyst:
Apart from what Shotgun Julia and Valmar said, this line is it for me (the 'Solution'):
We harvest advanced civilisations, leaving the younger ones alone
Ok? Even if we take the 'problem' of mass genocidal AI as given and accept that the harvest somehow preserves species, this statement is simply wrong and a Lie!
As per several Planet descriptions in ME2 (I believe also in ME1) Reapers are responsible for the orbital bombardment of several pre-spaceflight civilisations!
At least one bronze-age civilisation among those. A single Reaper could have landed and harvested the entire population, orbital bombardment is unnecessary in this case.
The only reason to bombard such a civilisation would be to either destroy them completely (nice 'harvest' - or was that the 'leaving along' the AI spoke of?) , or to hide evidence of said civilisation and the harvest. If it is the second one the reapers failed remarkably (Thanix bombardment marks on garden planets are oh so common, pluspoints for still leaving behind evidence of the inhabitants)!
Even if I disregard that, the 'solution' just does not work as solution to the 'problem' (it isn't even a bad solution, its only bad).
To prevent the (non harvest)destruction of species, the Reapers built the relay network, thus making it much easier and likely for less advanced and civilized* species to come in contact with one another and begin a genocidal war among themselves, ending in the (non harvested) destruction of one side!
If a species builds an AI force that is able and willing to wipe its creators out, the thread that this AI will wipe out other species is with relay network much higher than without!
Without the Relays, the probability of different sentient species coming in contact with another would be way lower. And if they establish some form of contact, the longer civilisation period needed to establish this makes it more unlikely that they attack the other side.
The relay network would only make sense, if the Reapers would use it as a detection system and immediately begin the harvest of any species advanced enough to use a relay. Instead the Reapers hide for ~50K years.
This means [headcanon ahead!] that the cycle is not about preservation, but to make sure that harvest-able species are widespread enough to build a minimum number of new Reapers per cycle. At the same time the species are (very likely) not technological developed enough to pose a real threat to the Reaper forces.
In short, the cycles are about reproduction -nothing else.
*Common theory that technological progress and civilisation development (getting more peaceful) are somewhat interconnected. I believe Mordin said something similar in regard to the Krogan, so the theory seems accepted in the MEU.
I 'fix' it by imagining that Sovereign is the Intelligence[...]
Nice headcanon(may I steal it?)!
The only problems that I see are that the Catalyst speaks completely different than Sovereign, and that the Citadel would have needed the proper equipment to run a Reapermind, without actually doing so before Sovereign connected. Then we are again at the point of: "If it can, why doesn't it do it that already?"
Edit: I'm fully aware that I just posted in the other thread that I'm tired of ending discussion... 
Modifié par KrrKs, 22 février 2015 - 01:57 .