I think quirks is understating it. The problem with appcache is that if you run into many of those gotchas the article lays out, it's often difficult to resolve them for previous users. For example, say you accidentally give the manifest a far-future expires (gotcha #4); users with the forever-cached appcache need to manually clear their cache in order to get things working again. And, depending on how you've structured your app, even explaining to users that they need to clear their cache could be difficult...

You really need to plan ahead carefully if you're using the appcache, which I think changes the definition from "a nice tool, with some quirks" to "a complicated feature that you have to understand completely before implementing."

With that in mind, I think bootup.js is an interesting alternative if you can work around its other deficiencies.