I'd imagine this has already been said within the 4 pages of comments, but in case it hasn't, here it is:
From what I've noticed the complaint isn't about the Catalyst as a character, it's how that scene was carried out. You only get one or two dialogue options and people thought it was very out-of-character for Shepard - who is naturally a very inquisitive person who likes to investigate - to just accept everything that the Catalyst has to say at face value. Why can't you ask him "Where the FUCK did you come from?! Who the FUCK built the Reapers?! What the FUCK is going on here, damnit?!" Obviously I doubt a half-dead Shepard would be dropping F-Bombs, but you get the point.
Had the scene (and really the ending as a whole) been executed better, I think people wouldn't have had a problem with Space Ghost Timmy.
And just for the record, everyone applying to the hypocritical notion of the "Yo' dawg! I heard you didn't want to get killed by Synthetics so I sent some Synthetics to kill you!" Apparently you're forgetting a key part of the story: not all organic races are harvested.
The plan as laid out - use synthetics to harvest advanced organic life so they never develop synthetics that end all organic life - does indeed make sense.
Your goal: create a solution that prevents synthetics from ever being developed and killing all organic life in the galaxy.
Your means: a fleet of nigh-invincible synthetic spaceships capable of harvesting organic races and turning them into more giant nigh-invincible spaceships. You leave races that have not yet advanced to grow into the next cycle.
Reason to your means: synthetic life is immortal, and as such your solution can last eternally.
In summation: it's either get harvested while
leaving undeveloped races alone, or have synthetics advance and eventually wipe out
all organic life. The only way to ensure that your cycle continues is by using things that can last for eternity...that is to say: synthetics.
Is it convoluted? Yes. Do I agree with the reasoning? No. However the plan does make sense.