There was a very nice system, including PIN numbers to manage the POS terminals. Way back when stock trade was 49$, it was 25 cent per transaction irrespective of the size of transaction. This should have become zero. But that is not what happened.
The 25 cent transaction fee is charged by the acquiring bank, not Visa and Mastercard - whose fees for debit are typically 1 cent per transaction as they are a volume based business.
The reason that acquirers charge is because they incur costs associated with that transaction (including, but not limited to, interchange fees). If they didn't charge, it would fail as a viable business model.
Pre-paid cards still have to use Visa or MC to get the request for the money from the acquirer (who has the relationship with the merchant and typically provides the terminal) to the card issuer (the bank that supplied the pre-paid card).
Regarding AppStore vs MC+Visa, in order for Apple to be able to accept payments directly they would have to get an e-money licence so they could issue virtual debit or credit cards for use on their phones. By doing so, they'd still need the rails that Visa and MC provide - unless they really want to get into the business of connecting themselves to all the banks worldwide (aka becoming a payment processor).