I feel like the author was primarily interested in his alchemical physics; the quintessence, how it works, how it interacts with everything. The rest of the plot was added so that he could keep playing with sulfur and mercury -- added piecewise, I suspect. When the good doctor's strained marriage and tragic backstory weren't enough to keep the travelogue-with-alchemy in gear, we got a headstrong daughter, an impromptu scientific society, a first-contact story, and the Inquisition. In some order. The plot threads keep crowding each other out; the alchemy is what sticks around, which is why I say it's the author's favorite.
Yes, I've written IF this way -- fair enough. At least in the game domain, I can keep your interest by letting you play with the quintessence. When my various plot threads aren't solid enough, people call me on it, and I'm calling this book on it. Nothing's terrible, and I got to the end in good order, but nothing in the story is quite fully-assed, either.
Furthermore: you know I said I was sick of the Evil Repressive Fundamentalist Church Story? Bringing in the actual Spanish Inquisition does not reconcile me to the trope.