The web is a fully cross-platform/cross-device, installation-free, and open-standards-based platform.
Although traditional GUI toolkits can chip away at different aspects of this, it is actually a much more intractable problem for them to solve than the aspects you cite as native desktop apps being better at. For example, interoperability between web apps has gotten steadily better as HTTP APIs have evolved, today's generation of web apps often make interoperability a selling point (Slack is a good example). From a traditional single-platform native developer the mechanism for this looks crufty and ill-defined, but that is the price you pay for a truly open standard not controlled by a monolithic entity. For instance, for all the beauty and elegance of Microsoft Visual Studio, there is no way they can bring that experience to OS X and Linux, let alone all the mobile platforms.
Native app developers have been wringing their hands over the "inferiority" of the web for 15 years now, but all the while ignoring that the web does something which no technology has ever done in terms of ubiquity. And what enabled this was the trojan horse of HTML/HTTP's initial simplicity. Hell, the simple HTML documents for which the format is ideally suited still outnumber apps by an order of magnitude, but the beauty is you have one platform that can support everything on the complexity continuum from the simplest documents all the way up to sophisticated business apps.