It's like the uncanny valley where humanoid things get so close to being fully realistic that the small difference in their behavior or look & feel causes people to be totally turned off. If it looks like a native app but doesn't quite behave like one, it's noticeable and (at least the people I've talked with) do not like it.
Maybe the HTML5 experience isn't good enough, but it truly sucks to have to write the app once for each platform.
I'd love to see the specific examples you're talking about; details like whether the apps were made by people with equivalent skills, and whether you're REALLY talking about the same app being judged better or worse.
Because it's so easy to write HTML5 and JavaScript, well, lots of idiots do it. If the study compares an app written by a median HTML5/JavaScript app developer with an app written by a median ObjectiveC developer, then it's not the environment you're actually comparing.
You can't get the best experience for each platform if the tools and frameworks you use are dumbed down to accommodate the lowest common shared experience across everything.
I agree that some UI changes are necessary between platforms as different as the PC, the Wii, and a touch-screen-based phone. But I very much disagree that you can't take advantage of solid cross-platform tools. I've written such tools, in fact.
Some native code to interface to native UI is necessary, but none of the native UI is really rocket science, and something offered natively on one phone can typically be done manually on another. Then it becomes an abstraction in the cross-platform library, and your code doesn't need to know how it's implemented.
But then again I'm a game developer, so I guess you've admitted that I could potentially already understand cross-platform development. ;)
I am planning on having a Web-app component to my next product, actually, and have been reading about them all; Dojo and jQuery Mobile are the two finalists I'm considering.
But the primary app is a game, and the production values for games make doing them entirely as web apps not an option.
Clunky scrolling would be a problem, sure, as well as choppy animations. I'll have to see what can be done when I actually dive in to writing the HTML5/CSS components.
The thing is, it's certainly POSSIBLE for web apps to animate better than they do. It may not be time for web apps to take over on phones, but it's only a matter of time. Processors in phones are getting more powerful, and the WebKit-based browsers are being optimized; scrolling animations really shouldn't be significantly slower done in JavaScript than they are in, e.g., Java on Android.