But what incentives will exactly cause developers to continue to develop web pages wherever possible instead of bundling everything into apps? Website owners also like the power that they can get from executing full-blown programs on each client's machine, rather than serving dumb unidirectional data. The Internet has evolved in many ways just like the outside world has evolved, IMO. The "correct" or the "elegant" is rarely what actually seems to happen. Instead it's a wild struggle for survival in which boundaries are pushed and abused, which leads to wonderful innovations, but the downside is there's nothing "ethical" about it.
The problem is that hosts have too much control over client's experience. Frankly, most of the works designers today do on the web is work that should not be done - 90% of websites would be infinitely better if they only sent text with lightweight semantic annotations and a list of available actions. The user should be able to explore the data in whatever way they please, and not be shoehorned into a single prescribed way of interaction.
That said, your point on incentives is spot-on. People making money on the web benefit from any marginal increase of control they can get - so the whole thing turns into a typical race to the bottom. And then, they also can (and do) use their money to influence the development of web technologies to make it easier for them to make more money. This process sadly isn't any different than regulations being influenced by businesses to benefit them instead of society.
Is there a solution? I don't know. Most people don't even realize how much of their own time and potential they waste by accepting the "status quo". I hope someone eventually develops a browser with sole purpose of unfucking the Internet. Some kind of a cross between links, Emacs and the Reader Mode from Firefox.
Web pages should use JS only when necessary to enhance the user experience.
Web applications can go hog wild and load 10MB of JS libs.