IIRC, this is regulation DD, and is quite a traditional rule. On the books, banks account for savings and checking funds separately, and have separate capitalization requirements because checking accounts are assumed to be more liquid.

Under these circumstances, you don't want consumers to treat savings accounts like checking accounts (which they have an incentive to do, because of traditionally higher interest rates), so you create a disincentive through transaction limits.

For BankSimple, this is probably not much of a problem. Reg DD allows for more than six transactions if you charge a per-transaction fee. Most banks charge a buck or two (or $25), I'm not sure if there's any regulatory problem with them dropping the fee to $.01 or $.001