By black goo, are you referring to the underground maze in the Aztec level or the shadow Max segment in The Gauntlet (final chapter)?
I mean the Gauntlet. The navigation system isn't working for me at all here--Max keeps stepping in the wrong places.
My take on the Aztec level was that from the reality flashbacks DNAV (or something similar) had actually struck Aztec society, and that was the direction of research Max had originally taken when trying to find a cure, and information he gained through that research was what eventually brought him to the insight that resulted in the cure (in one of the flashbacks he looks at a picture taken when he was looking into the Aztec angle, then exclaims "Of course!").
The Aztec chapter was the only dreamworld that I really struggled with. There's a reference to the Aztecs in one of the cutscenes where Max states something to the effect of the Aztecs having managed to survive a plague without the aid of modern medicine. Then you get another segment later on when Max seems to have an epiphany while looking at an old photo of an Aztec ruin; that's when the idea for the cure dawns upon him. It's definitely not explained all too well, and I can wholeheartedly agree that this is easily the weakest part of the game.
Both of you have interesting theories about the Aztec level, but it still failed to engage me on an emotional level. I think its relationship to Max's psyche is a bit tenuous even if you're right.
Then there were the levels that were obviously relevant, but the execution of which seemed off to me. The cyclops level, for instance . . . yes, I see how the cyclops figure was important to Max, since he was the hero of a comic book that Max read while his sister was dying and he felt helpless. But I thought the actual level got bogged down in detail about the war between the cyclops/centaur people and the insects. I also thought that level looked ugly and didn't have very interesting puzzles, which detracted from my immersion in Max's consciousness.
Overall, I thought the game was good--but since I often see it listed as one of the best adventure or horror games ever, I think my expectations were too high.