I disagree with the majority of this article.
"being nagged to install your damn apps." - This doesn't make sense to me. As a developer myself, I can say that if I created an app, I would try to advertise it to my customers. Also, if you frequently visit sites like Amazon, Netflix, or eBay, wouldn't you want to know that there's an app available for the site that makes it more convenient to launch and navigate? As a developer, there's no better way of advertising to your customers than promoting your products on your own web page. Is it annoying? Yes, but no more annoying than any other ad I encounter.
Millions of pointless apps - This doesn't make sense either. Having an abundance of apps is a GOOD thing. How is it ever a bad thing? Every person I know who owns a smartphone uses a few core apps (Facebook, YouTube, Pandora, etc), and then they have dozens of peculiar, weird, random apps that I've never heard of that PERSONALLY SUITS THEIR TASTE. That's the beauty of having a million apps - there's a greater chance that an app exists to your particular desire. Taking this away would make us move backwards, not forwards.
Fragmentation into parallel and incompatible app worlds - This I somewhat agree with, but this problem has existed before. When you code for a website, you have to make sure that it's compatible for IE, Chrome, Firefox, etc. When you write an x86 program, most people just assume it's for Windows, they don't even realize it's probably not available for Unix, Linux, OSX, or some weird random OS out there. I guess what I'm trying to say is, this is nothing new, fragmentation has existed forever. Except this time, we aren't dominated by a single OS (Windows during the 80's/90's/00's) but instead we're facing a two-party OS dominance (iOS and Android), with iOS being more fragmented I'd say, since all apps for iOS have to be coded for the different resolutions of each device, whereas in Android the resolution scales natively.
Paying for apps became a race to the bottom, When apps are free, you're the product - This has less to do with apps and more with how supply/demand works. When apps are in over supply, there's more competition, the price will lower, and developers will have to think of ways to generate revenue (ads, in-app purchases). When apps are in short supply (think back to the mid 90's) people won't hesitate to spend $50 on an antivirus because they don't know of any other software that's equivalent.
The app user experience is wildly inconsistent - This I agree with. This is more of a developer problem. Make your apps more consistent, developers.
The World Wide App - This may be the solution to everything, actually. Just make all apps HTML5 based and increase HTML5's functionality. No more Java/XML for Android. No more... whatever they use for iOS. No more C#/Javascript for Windows Store apps. Let's just have one unified programming language that will be accessible on any and all devices.