If the web browsers would provide _some API_ for persistent storage without yanking the carpet out from underneath developers this wouldn't be such a huge problem. There _used_ to be a file-access API but it was removed.
Personally, I think web browsers are too large a surface area to secure/keep secure and the world is probably going to swing the opposite direction to native, downloadable applications without the interference of a third-party store.
Wait, you think downloadable native apps without any intermediary to validate them is more secure? What you're describing is basically the old shareware system, which was riddled with security issues.