Traditional credit card processors are able to settle accounts daily. It remains to be seen if Square will offer a similar service. Many established merchants (especially restaurants) desire what is called "real-time billing" or getting cash in the bank once the card is swiped rather than waiting for payment to be deposited or settled.
The other problem is that Square accepts anyone. The reason its difficult to get a merchant account through other payment processors is because chargebacks ARE EXPENSIVE. (payment processors will not accept a merchant that is above a 2% chargeback rate). This means that Square will be susceptible to a larger amount of chargebacks (which means that most of their angel funding will likely be in an escrow account to protect against chargebacks).
Great idea but we'll see how these issues are handled.