In retrospect, I think this would have been a better order of exposition for the monadology article:

1. Start with a general discussion of the wavefunction of the brain, implicitly within a many-worlds framework, i.e. nothing about collapse. Most of us here will agree that this ought to be a conceptually valid enterprise, though irrelevant to biology because of decoherence.

2. Next, bring up the possibility of quantum effects being relevant to the brain's information processing after all. In the absence of specific evidence, readers might be skeptical, but it's still a logically valid concept, a what-if that doesn't break any laws of physics.

3. Next, try to convey the modification to the quantum formalism that I described, whereby fundamental degrees of freedom (such as string-theoretic D0-branes) become entangled in island sets that are disentangled from everything else. (The usual situation is that everything is entangled with everything else, albeit to a vanishingly small degree.) There might be a few more frowns at this point, perplexed wondering as to where this is all leading, but it's still just mathematics.

4. And finally say, these island sets are "monads", and your subjective experience is the inner state of one big monad, and the actual qualities and relations which make up reality (at least in this case) are the ones which are subjectively manifest, rather than the abstractions we use for formal representation and calculation. This is the part that sounds like "woo", where all these strange ologies like ontology, phenomenology, and monadology, show up, and it's the part which is getting the strongest negative reaction.

In privately developing these ideas I started with the phenomenology, and worked backwards from there towards the science we have, but an exposition which started with the science we have and incrementally modified it towards the phenomenology might at least have made 3/4ths of the framework sound comprehensible (the three steps where it's all still just mathematics).

Then again, by starting in the middle and emphasizing the ontological issues, at least everyone got an early taste of the poison pill beneath the mathematical chocolate. Which might be regarded as a better outcome, if you want to keep woo out of your system at all costs.