Re: I don't see the problem
I see what you are saying there.
As soon as most users will be on the "web of apps" rather the "web of websites", in site ads market will crumble and in apps ads market will skyrocket, much more invasive than any googleads-filled page or bundled installer.
I already see this happening on most free Andorid and iOS apps, and MS Store is heading this way... not too fast, it seems, but only as people don't really like what is happening, and consumerization is a big drawback for corporate users; anyway it is where IT is heading to.
But if it is not good news for traditional - legacy :P - websites, I think it is not a good thing for apps developers too, as Store-centic distribution effectively transform a indie developer in a marketing research drone for the Store owner.
Is your app successful? Does your app threaten one of my apps (Office, IE...)? Ok, now you can do business solely from MY store, so be ready to be flooded by one stars, being placed in second page, the key API you use to be deprecated, or your software to be outright banned.
Plain and simple.
This means software will be less free as in freedom, and less "business" to.