I've never liked AIR and QT/WebKit apps (or even the Opera web browser) because there's this feeling similar to that of Uncanny Valley, where something just doesn't feel right. The scroll bar doesn't work well, something happens too fast or too slow, selection doesn't behave as it should, the buttons look weird. Something along those lines.
I think "Uncanny Valley" is exactly right. It was something we faced when building an AIR app, we could mimic the look of the each OS pretty closely but it never felt quite right.
In the end we opted to a stylize feel of each OS but not an attempt to recreate the look and feel exactly.
I second that, Uncanny Valley is exactly it. It was the same a few years ago on the web when web apps tried to duplicate native functionality (think filebrowsers etc.), it never worked right. In fact, Dropbox (however much I love it) still has that problem in their web UI.
I think the point he's making is that a lot of the UI elements don't quite look or feel right, kind of like how a lot of Adobe CS apps have "native" dialogues full of weird mistakes.
Sometimes little look and feel things have a huge impact on how people react to apps: I remember (and I could be wrong, it's been a while) pretty much instantly not liking Opera on OS X when I first tried it since it had smooth scrolling turned on by default, something almost no Cocoa apps do.
