I've written about this before on this thread and just now on another, but I wanted to share it on here and further expand on what I consider to be a serious problem with the Reapers and introducing a motive for their actions whether it be the existence of the Catalyst as AI (creating synthetics to kill organics so synthetics don't kill organics) or the original dark matter story.
Let's consider everything the Reapers have stated in regards to their state of existence and relationship with organics in the Galaxy. Take note at how the introduction of the Catalyst as an AI, and what it says COMPLETELY contradicts everything the Reapers have said in Mass Effect 1 and 2:
Sovereign:
"We impose order on the chaos of organic evolution. You exist because we allow it, and you will end because we demand it."
Sovereign:
"Rudimentary creatures of blood and flesh. You touch my mind, fumbling in ignorance, incapable of understanding."
Sovereign:
"There is a realm of existence so far beyond your own you cannot even
imagine it. I am beyond your comprehension. I am Sovereign."
Sovereign:
"Organic life is nothing but a genetic mutation, an accident. Your lives
are measured in years and decades. You wither and die. We are eternal,
the pinnacle of evolution and existence. Before us, you are nothing.
Your extinction is inevitable. We are the end of everything."
Sovereign:
""Your civilization is based on the technology of the mass relays. Our
technology. By using it, your civilization develops along the paths we
desire. We impose order on the chaos of organic life. You exist because
we allow it, and you will end because we demand it."
Sovereign:
"My kind transcends your very understanding. We are each a nation -
independent, free of all weakness. You cannot grasp the nature of our
existence."
In my opinion, there is no
enemy more intimidating than one whose logic or better yet existence you
cannot comprehend. The Reapers were introduced in Mass Effect as
literal grim reapers (no pun intended) who represent being of seemingly
infinite powerful that we have nearly no hope of being able to defeat.
They want our destruction and arrogantly hold us so far beneath their
contempt that we are unworthy of even being given some form of
explanation.
Their relationship with us is best thought of
being similar to the one we as humans typically have with insects within
our home. When an insect is inside a person's home, the human is most
likely going to kill the insect without a moment of hesitation. Why
though? It is because we as humans hold the insect as being so
infinitely inferior to us, that killing it because it is inside our home
is not worth an explanation. Thus is it so with the Reapers and us in
the game. The Galaxy is the Reapers' "home", and we are the insects. We
are regarded as being so inferior to them that they feel there is no
need for an explanation as to why they are killing us.
With the
introduction of a motive, Bioware committed the largest mistake a
writer(s) can make when designing a villain: they tried to humanize a
villain who up until now has been designed to be the exact opposite of
being worthy of empathy. When designing a villain, the very first thing
that is done is you deprive them of anything that the average player,
reader, viewer, etc can relate to in a positive way. You make them ugly,
arrogant, lustful for power, etc. It makes it easier for the villain to
be hated and gives the player greater incentive to want to defeat them
in the end. Humanizing the Reaper completely wipes out this concept that
the entire series has been reinforcing, and seemingly it was done for nothing more than "surprise twist!" shock factor. It completely contradicts EVERYTHING that has been stated by Sovereign and Harbinger.
The
introduction of the Catalyst as an AI who controls the Reapers creates a
mass of problems in the form of contradictions and plot holes. It
effectively reduces the Reapers from being powerful sentient machines to
seemingly the slaves of this single AI who is stuck in one place as the
Citadel. Take note at hoe Sovereign states they we evolve and develop
according to the path that they desire....errr....so why not have us develop down a
path that doesn't involve creating synthetics who kill so that you
don't have to commit genocide against us? Were the Reapers outright
lying to you throughout the entire trilogy or completely out of the loop on what their purpose was or just plain arrogant?
Was Sovereign just an idiot and that's why he was left as the
vanguard so the other Reapers did not have to deal with his senile statements? So much for them being these larger than life villains that
we are incapable of understanding.

The
Catalyst as an AI or/and the introduction of an understandable motive,
illogical or not, completely destroys the dynamic of the Reapers
established in the first two games. Bioware needs to stop trying to give
complexity to the Reaper when frankly, they don't need it to be great
villains. Bioware, leave the Reapers as the villains they were portrayed in Mass Effect 1 and 2, and it would save you a lot of grief in trying to explain the massive plot holes in the ending.