This is the age old question for app developers. To state my bias, I make a living creating mostly native app and the occasional web app, but I greatly prefer working on native apps. I'll be referring to iOS devices for all of this, but it applies to the Mac (sorta, see the end), Android, and almost any other platform.
We can all agree that native apps have a much better experience than web apps, especially on slower devices (like the iPhone). Pull up your contacts in your iPhone and flick through them really fast. See how smooth that was. Now pull up any website and do the same. Not so smooth. Checkout Cover Flow in the iPod app. Amazing, right? Show me a website that does that that smooth. You can't.
The reason that native apps greatly out perform web apps is that there is a lot more processing power used to render website than it is to render native apps because they are... well, native. Websites need to run through some sort of engine, in this case WebKit, to convert them to something that can be used by the device.
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