The difference between a native iOS app and a fake app that's really just a wrapped web page is obvious. Native apps are a lot faster. It's possible there is some selection bias here and you only notice the web apps when they're bad, but I really don't think this is the case. Native apps just seem categorically better.
If Facebook pouring immense resources into it couldn't get web based mobile applications to be good, it's probably because the technology just can't compete with native.