They stuck with 30-pin because it was something their customer base had already bought into, and they didn't want to force a change. They went with Lightning because, let's be honest, micro-USB is shit — every micro-USB device I've owned has had the connector fail within two years. Lightning can handle 12W of power, micro-USB 9W. Lightning is reversible. Lightning has no moving parts on the connector, prone to breaking (or worse) grabbing onto your $700 device with a death grip and bring nigh-unremovable.
It would be great if they switched now to USB-C. They're clearly in the works on that, but didn't want to make a connector change on their phones after only two revs.