By "take the Catalyst's word for everything" are you referring to the Crucible's functioning, the Catalyst's own motivations, or both? The former is interesting for Shepard, but it's hard to construct any kind of plausible rationale for his statements to be lies. People often do try to construct some sort of rationale that lets them believe just enough of what he's saying to end up picking Destroy, but it's usually transparent nonsense.
I would have been much more comfortable with the idea that organics need to be protected from synthetics if we'd seen some that were actively hostile sans outside influence. What we actually saw in-game were Pinnochios, friends and allies, and synthetics trying to defend themselves. And the heretics, which were really no more dangerous than any other merc group - and perhaps less so than an organization like Cerberus.
From my perspective, the entire premise for the reaper's very existence was not effectively demonstrated in-game. In fact, I'd say a genophage-free Krogan population could represent a bigger threat.
The Catalyst actually being right about anything besides the Crucible doing what he says it will do -- which he is right about about -- isn't necessary. If anything, ME3 undermines that, as you point out. But there's nothing wrong with the villain being wrong about stuff. Happens all the time.
I don't disagree with that; all Shepard really needs to know in that moment is her options.
Still, it's a huge info dump, some of which doesn't gel with what we've been shown throughout the trilogy. That's the basis of the "show, don't tell" comment. I very definitely had a WTF?! reaction to it the first time.
Playing through the Leviathan content prior to meeting the Catalyst makes for much better storytelling, imho.