Another developer whining that they don't have free range to do whatever they want.

There are a multitude of reasons why Apple doesn't allow Safari sites to do whatever, namely security, power management, feature duplication/user confusion, etc. When you pay to deploy a native app, you are paying for hosting, the reviewers, payments, availability, etc.

There is no control over when a website may change and at any time your server can be hijacked to distribute malicious content vs an app, which is much more protected by layers of security and process.

Your priorities are definitely not priorities of the end user, where Apple, a company that has millions of customers is. If they were irresponsible and distributed iOS in the way you want, it would be Windows XP all over again. Viruses, security holes daily, etc.