The problem with a "normal" app is now you are beholden to the rules/regulations/evaluations of a third party that can easily decide without recourse that your "app" should not be in their store. Even if your app "is fine" every update and upgrade incurs a delay through the third party's reviewing process before your users receive it.
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.