> A clean understandable web UI is good for a seldom used app, but a lot of the intranet apps are "constant use" and were faster to use in their legacy dos implementation than the newer web version. Browser hell just makes the problem worse.

This. Click, wait, click, wait, click, wait is in no way better than how quickly you can fly with a well memorized set of keyboard shortcuts in a native app.

This is not a web vs. native problem. You can implement keyboard shortcuts in a webapp. You can neglect to implement keyboard shortcuts in a native app.

This is all about attention to detail, which internal corporate apps almost always lack.

You can add keyboard shortcuts to a webapp. What you can't do is control or override the keyboard shortcuts that the browser adds, and you can't make use of the full suite of possible keyboard shortcuts. I've looked at adding shortcuts to my webapps many times over the years, and it's never been worth the effort because the result is just confusing to the user.

I use keyboard shortcuts extensively in gmail, jira, stash, and a bunch of other apps.

There's no problem implementing it. The designer should just think about it.

> (good multi screen/multi window support, better, good support for complex interactions like shortcuts, ctrl-clicks etc).

Totally do-able on the web. It's often the web apps architecture that prevents a good UX, not the browser's capabilities (which are really good now).

> Even on mobile […] we can't make web based apps that are better than native ones.

That's an issue of the developer, not the browser itself. I do admit that Safari/iOS is really hurting here but you can work around that if you really want to (it will still be a sub-par UX, though).