Web apps can’t use the iPhone’s multi-touch input method. That’s reason enough that web apps can’t be real apps on an iPhone.
From a more personal perspective, the lack of a “real” iPhone SDK wasn’t the part of the keynote that left the biggest impression. Rather, I couldn’t help but notice that the new Stacks feature looked an awful lot like Overflow. It is cool that enough people know about Overflow that I’m not the only one that noticed though (a few people at the conference have asked me about it as well – thanks for your concern!). After thinking about it for a few days, I think that Overflow hasn’t quite been Watson’d. There is a lot of stuff that Overflow does that Stacks doesn’t, and I think there is a lot that Overflow can do in the future to continue to innovate (to continue with the general overuse of that term). I get the impression that Stacks are meant to be used as more of a temporary holding place, whereas Overflow is much more configurable, accessible via a hot-key, and not something that you’ll likely want to change the contents of every day. The intended use of each turns out to be only slightly similar. Really they are more visually similar than conceptually similar.
Also, congratulations to all of the Apple Design Award winners, especially Panic / Coda for Best User Experience and MacRabit / CSSEdit for Best Developer Tool, both of which I think are just awesome, extremely useful applications with great UIs. Sandvox from Karelia (who also created Watson) got the runner up spot for Best User Experience, and although I’m not a target user, it’s also a really nice looking app.