I hate to rely on js for navigation, period; and I'm also guessing at some point that Google will be crawling js links.
Me too. Partly becasue it's not standard and I'd be doing it in this case, again, for SE reasons rather than because it makes any coding sense. And partly because of what you said about the SE's reading js.
marketers using multiple brands are trying to do something that's essentially similar to some using multiple sites... to catch eyeballs in lots of places.
Yes and not only that. It's also a user thing. One analogy that makes lots of sense to me is magazine publishing. A given publisher may put out a Golf magazine, a Tennis magazine and an Polo magazine. They don't bundle all three and tell you you should buy them as one magazine called "Sports for the Rich." Each is separate for a reason. Different audiences, different interests, different profiles. Yet the SE's would have site a site owner build one site and make the Tennis visitors navigate past Polo content. Or risk being penalized. Just plain goofy.
I understand that producing hundreds of hotel sites, one for each city, with identical templates and all interlinked causes problems for the SE's (I don't run any hotel reseller sites btw). But what if they are e-commerce sites and one is about widgets and one is about blammo's and widgets and blammo's have nothing to do with each other, and have very different user bases?
Or what if widgets and blammo's share intersecting but not identical user bases? If users of the widget site like the way the site is organized and like the way the cart works, and then learn by way of a link that the same publisher also makes a site for blammo's, they might like that site too. What if there are ten our twenty sites, all featuring very different products/services? Should a user who likes one not be made aware that the others exist too by some sort of nav structure?
There has to be a better way than just forcing them all out of the SERP's because they interlink, even if only conservatively.
One common refrain is just not always true: "Build sites for the user." Sometimes, it's all about the SE's. Sadly.