I have the same thoughts. Phones were too slow few years ago, web standards were not mature, so well written native apps were in obvious advantage. Now phones have proper CPUs, lots of RAM, so web apps for many tasks won't be distinguishable from native apps. Web standards are good too.

May be Apple will curate list of blessed websites and allow them to launch background services, using icloud payments, etc. This way they'll continue to have their cut and their control.