The performance of web apps is much worse than that of desktop apps, for example. Complex desktop apps written in C, VB, and PowerBuilder ran just fine on 486 or early Pentium systems that have a very small fraction of the processing power and resources of a modern system. Yet it's still common to see web apps in general perform quite poorly on these modern systems, while doing less than the mid-1990s apps did.
Developers at least have some choices when it comes to desktop apps. They can use a multitude of different languages, along with a variety of different libraries and frameworks. This is a much richer ecosystem than what we get with web development today, where you're basically stuck with JavaScript, or a language that's nothing more than a slight veneer over JavaScript (CoffeeScript, TypeScript, and even Dart). Don't even bother mentioning asm.js or Emscripten. Asm.js is merely a rancid subset of JavaScript, and Emscripten is experimental at best.
The portability argument isn't even valid. Languages like C, C++ and Python offer superb portability today, especially if used with one of the extremely cross-platform GUI toolkits available for making desktop apps. Given that almost every major JavaScript implementation today is written in C and/or C++, the portability of JavaScript is inherently no better than than of C and C++.
The ability to communicate over a network isn't anything special, either. All sorts of desktop apps have been doing this for several decades now.
The distribution argument also isn't valid. The package management systems offered by most Linux distributions, for example, are far nicer to work with. They make it trivial to find and install native apps, and unlike web apps, you get to choose if and when you upgrade, rather than having changes forced upon you time and time again.
The sandbox argument is also irrelevant. Various mainframe and UNIX-like OSes have offered several different ways of jailing or otherwise isolating processes for many, many years now. It's nothing new. But unlike the browser, they give real control over how much access is allowed, and without imposing horrid performance loss.
All of these limitations of web apps come together to make for a user experience that isn't enjoyable.
At best, web apps can imitate desktop apps, usually at a quality and user experience level 10 to 15 years behind desktop apps. It's objectively incorrect to claim that web apps "rival" desktop apps, when all of the evidence shows that they clearly do not.