Since playing through the Extended Cut and getting to know more about the Catalyst, I ended up thinking and that ended in an essay. It's not very long, I promise.

This contains major spoilers for Mass Effect 3.

So I've been thinking about how the Catalyst and the reapers and the whole synthetics vs. organics argument.  The Catalyst is basically an AI, created to solve the conflict between organics and synthetics, it said so itself.  And then it turned its own creators into the first reapers, involuntarily. They probably didn't fancy that idea, hell, it even told you that they didn't approve. The Catalyst also tells Shepard that the created will always rebel against their creators, which in a way is exactly what it did.

Which explains why the Catalyst is wrong, the reapers are not a solution at all, he himself is a part of the chaos he's trying to stop, and he simply doesn't understand it.  When explaining synthesis he says that synthetics seek to understand organics. He is a synthetic, so according to his own arguing he does not understand organics.  So when he says that the Reaper conflict isn't war, he can only see it from a synthetic perspective.  His argument is invalid.

Look at the geth/quarian conflict, it was possible for Shepard to resolve it peacefully, and even if future problems arise, they too could end nicely for everyone.  Sure, the Catalyst is old and all that, but if it wipes out civilizations before they get much of a chance to figure things out themselves, then how could it know for sure what was going to happen?

Also, the Catalyst finds synthesis the best new solution, maybe it does not wish to be destroyed along all other synthetics or controlled by something else. Everything, whether synthetic or organic, wants to survive. Even the Catalyst should have that desire. Merging is a better option for synthetic life to remain. If you argue with him after discussing control, he says that he'd rather not be replaced, but will be forced to accept it if you choose so. Notice, he doesn't say he accepts it but that he will be forced to. After that, he hurries to give his final option, stating it as inevitable and perfect. Keep in mind that this thing is an AI and the collective mind of all Reapers and that synthesis is basically what Saren Arterius, the villain in Mass Effect 1, sought.  The Catalyst may disguise itself as a kid Shepard failed to save, but I'd say that's mostly to make it more persuadable. If it talked with Harbinger's voice I doubt Shepard would be inclined to believe a word. And if you reject the choices, it reveals this, the "So be it" showed its true self. When asked about its creation, it doesn't explain much or give details, maybe to protect itself from Shepard's reaction if he/she knew the truth.

Now let's get back to the point.  If the Catalyst is a synthetic, then how can it be reliable in the conflict, how can it be completely impartial? It isn't, and that reflects in its words. Maybe it even thinks of itself as the good guy, I'm actually sure of it. It gives Shepard some room to maneuver, a few choices, but when pushed simply walks off like a stubborn child. (If Shepard shot him, I can understand, but refusing to accept paths that are being forced upon you and wanting to find a better way out than those given to you isn't reason enough to say "screw you" and run off without considering that there might be something to it.)