While Nilay's article is a bit hit and miss, it still seems pretty undeniable to me that the mobile web experience is inferior to native apps.
I don't think mobile safari can be blamed. When the iphone was first released, people thought safari on it was amazing. Today's safari is a much better browser, running on vastly superior hardware, but the browsing experience is inferior. Who else is to blame but the content providers?
For the most part, I haven't seen a technical superiority between web & native for most of what folks want to do. It seems more a practical superiority because we haven't been allowed to / found a need to crap up the native experience quite as much.
App stores & in-app purchases go a lot way toward obviating the need for so much cruft. Too much JS framework cruft is a self-inflicted injury. These are addressable issues, not inherent to the web.