I'm wondering how this will eventually play out if most companies start requiring Apple/Google to allow third-party apps to use their own payment system.

The commission fee that Apple charges, 30% is partially to cover operating/marketing etc. Obviously, Apple makes a good profit off the App Store these days, even though Jobs said he'd be happy if it was break even at best.

Here's an analogy I've been thinking on about this whole thing. The iPhone (or whatever phone you want) is the equivalent of a Walmart store. If you want your product to be sold in Walmart, you have to send it to their distribution center (ie App Store) and Walmart will handle sending that product out, etc. Walmart will handle the credit card transactions, etc and pay you the negotiated rate for your product (Yes, odds are Walmart buys your product first, then sells it, but with credit lines, etc it's almost the same thing).

Does Walmart allow you to go in, put your product in the store and sit there with a square device and sell your stuff? Amazon is more analogous of physical to app in the sense that Amazon is the transaction point but may or may not actually maintain control of the product.

So what's the end game? I suspect if Apple/Google has to allow developers to collect their own fees, Apple will start charging paid apps to be in the App store.

They will continue to allow free apps to be shown, but if you want to charge for your App either one time or subscription, you'll have to pay an upfront fee to be listed.

And that charge may depend on the number of downloads.