What if an independent app store, fails at adequately stopping malware from getting through? Is Apple going to ban the entire store then? Does Apple get to do that job for those stores instead? If the latter, does the App get reviewed both by Apple and the independent store? Does Apple get a cut in that scenario?

How do you install independent app stores to begin with? Do you install them with he App Store? That would put them at a disadvantage similar to how Microsoft put other Browsers at a disadvantage with IE. Do you provide a choice then when you setup the phone?

Purely from an anti-trust perspective I can see why the idea of independent app stores might seem appealing at first glance. Thinking about this just for a moment brings up so many questions though and I don't see how you can possibly come up with satisfying answers that lead to good security and a good user experience.