You're right that things like PhoneGap give access to native features. However, the Native-API-implementations in these frameworks are 1) typically significantly behind the native OS (release date) 2) tend to have less-than-feature-parity
So, often you're stuck writing your own native bridge, or tweaking the portability framework's version, which is time wasted (IMO) vs writing to the native framework. As an example, just try and write a PhoneGap app using Bluetooth: The Android implementation is incomplete, and the iOS version is non-existent.
Also, there are a tonne of performance issues you run into with the HTML/CSS/JS + Framework + Native solutions. As a thought experiment, consider how you'd build Instagram in one of these frameworks.
1) Image filters in HTML/CSS/JS land? Slow. 2) Thousands of images in a continuous virtual scrolling window in HTML land? Slow. 3) Fetching a binary blob (the image) from the OS, and throwing the resulting blob back-and-forth to web-land (for example, to use HTML5 offline storage) ... hellish slow.
Compare that to native... it's just one example of where the theory of HTML for UI and native for logic breaks down when you start to push the platform a little outside it's comfort zone.
The Flickr web interface definitely needs a modern browser (Chrome or the latest Firefox), otherwise it will choke from time to time, however that's to be expected when you're basically playing around with 10,000 photos. For me it does a spectacular job, more so than some native apps I tried (granted, I never tried Adobe Lightroom).
Thousands of images in a continuous virtual scrolling
window in HTML land? Slow.
You can use the same tricks you'd use in a native app, such as loading only the thumbnails that are currently visible in the user's window.http://www.vasantkumar.ca/2012/08/native-vs-html5-why-facebo...
But simply saying "They removed HTML5 and all works a lot better" is very wrong.