I'm fairly sure this problem of traditional inputs has nothing to do with Apple's exclusion of Flash. Many web-sites also use ui interactions like mouseovers

I'm fairly sure this problem of traditional inputs has nothing to do with Apple's exclusion of Flash. Many web-sites also use ui interactions like mouseovers and there are many bad designers that fail to make their sites degrade gracefully. Following your logic, Apple would ban web sites as well because they might not just work. Now let me check-off 'Dead horse thoroughly kicked' from my list of things to do today.